Ben Bolstad
| Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_19 |
| git_last_commit: af6c73d |
| git_last_commit_date: 2024-04-30 10:16:21 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-28 17:41 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 249/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.68.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.68.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BufferedMatrix_1.68.0.tar.gz |
| StartedAt: 2024-06-26 23:39:26 -0400 (Wed, 26 Jun 2024) |
| EndedAt: 2024-06-26 23:41:04 -0400 (Wed, 26 Jun 2024) |
| EllapsedTime: 97.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BufferedMatrix_1.68.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BufferedMatrix/DESCRIPTION' ... OK
* this is package 'BufferedMatrix' version '1.68.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BufferedMatrix' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/BufferedMatrix/libs/x64/BufferedMatrix.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'Rcodetesting.R'
Running 'c_code_level_tests.R'
Running 'objectTesting.R'
Running 'rawCalltesting.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/00check.log'
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'BufferedMatrix' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function 'dbm_ReadOnlyMode':
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: 'sort_double' defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
gcc -shared -s -static-libgcc -o BufferedMatrix.dll tmp.def RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'rowMeans' in package 'BufferedMatrix'
Creating a new generic function for 'rowSums' in package 'BufferedMatrix'
Creating a new generic function for 'colMeans' in package 'BufferedMatrix'
Creating a new generic function for 'colSums' in package 'BufferedMatrix'
Creating a generic function for 'ncol' from package 'base' in package 'BufferedMatrix'
Creating a generic function for 'nrow' from package 'base' in package 'BufferedMatrix'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.28 0.17 0.65
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 468464 25.1 1021761 54.6 633414 33.9
Vcells 853870 6.6 8388608 64.0 2003138 15.3
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Wed Jun 26 23:39:58 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Wed Jun 26 23:39:58 2024"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x000001d306cfda70>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Wed Jun 26 23:40:09 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Wed Jun 26 23:40:12 2024"
>
> ColMode(tmp2)
<pointer: 0x000001d306cfda70>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.7622728 1.2793917 1.0496495 -0.6483189
[2,] -0.1095212 0.8021277 0.7596662 1.8893380
[3,] 0.1873436 1.7597839 0.2408761 1.4815866
[4,] 1.0086656 0.3736617 0.4701205 0.6368740
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.7622728 1.2793917 1.0496495 0.6483189
[2,] 0.1095212 0.8021277 0.7596662 1.8893380
[3,] 0.1873436 1.7597839 0.2408761 1.4815866
[4,] 1.0086656 0.3736617 0.4701205 0.6368740
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9881066 1.1311020 1.0245241 0.8051825
[2,] 0.3309398 0.8956158 0.8715883 1.3745319
[3,] 0.4328321 1.3265685 0.4907913 1.2172044
[4,] 1.0043234 0.6112788 0.6856534 0.7980438
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 224.64334 37.59041 36.29489 33.70014
[2,] 28.41892 34.75829 34.47555 40.63466
[3,] 29.51566 40.02547 30.14879 38.65363
[4,] 36.05190 31.48645 32.32665 33.61731
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x000001d306cfdad0>
> exp(tmp5)
<pointer: 0x000001d306cfdad0>
> log(tmp5,2)
<pointer: 0x000001d306cfdad0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 467.5657
> Min(tmp5)
[1] 53.02462
> mean(tmp5)
[1] 72.24446
> Sum(tmp5)
[1] 14448.89
> Var(tmp5)
[1] 855.9834
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.44677 69.90239 69.73299 70.94464 70.55756 70.45801 68.19547 69.93804
[9] 72.57970 68.68901
> rowSums(tmp5)
[1] 1828.935 1398.048 1394.660 1418.893 1411.151 1409.160 1363.909 1398.761
[9] 1451.594 1373.780
> rowVars(tmp5)
[1] 7887.98619 58.67766 87.47355 69.72406 57.42052 81.92032
[7] 83.79517 68.58403 55.90186 68.85265
> rowSd(tmp5)
[1] 88.814336 7.660134 9.352729 8.350093 7.577633 9.050984 9.153970
[8] 8.281548 7.476755 8.297749
> rowMax(tmp5)
[1] 467.56568 88.73694 92.30858 89.60406 85.34730 85.15058 82.21749
[8] 81.58454 83.24788 87.89538
> rowMin(tmp5)
[1] 57.38617 59.15026 53.27021 55.98912 58.23828 53.02462 54.30289 56.32422
[9] 57.05620 56.32756
>
> colMeans(tmp5)
[1] 109.11947 71.50616 69.79455 70.88571 65.12370 70.59601 73.59373
[8] 68.64865 71.11299 69.78600 68.10343 68.69846 72.40651 69.87817
[15] 70.51680 70.52389 72.24608 70.43260 70.01880 71.89744
> colSums(tmp5)
[1] 1091.1947 715.0616 697.9455 708.8571 651.2370 705.9601 735.9373
[8] 686.4865 711.1299 697.8600 681.0343 686.9846 724.0651 698.7817
[15] 705.1680 705.2389 722.4608 704.3260 700.1880 718.9744
> colVars(tmp5)
[1] 15917.14286 78.89909 32.52788 81.46703 47.72819 55.29288
[7] 64.41836 99.30827 74.90775 99.19606 56.91248 72.00642
[13] 81.98567 69.52301 76.84670 54.35125 66.47295 88.61340
[19] 42.90383 107.00971
> colSd(tmp5)
[1] 126.163160 8.882516 5.703322 9.025909 6.908559 7.435919
[7] 8.026105 9.965353 8.654926 9.959722 7.544036 8.485660
[13] 9.054594 8.338046 8.766225 7.372330 8.153094 9.413469
[19] 6.550101 10.344550
> colMax(tmp5)
[1] 467.56568 83.30777 76.60757 84.57572 76.01868 78.86156 92.30858
[8] 85.34730 83.43183 83.56569 83.24788 81.32268 88.73694 87.89538
[15] 82.77274 81.28790 84.89429 85.15058 77.43920 89.60406
> colMin(tmp5)
[1] 59.15026 56.32756 58.20990 60.22324 54.30289 59.07029 62.04375 53.02462
[9] 58.30325 55.50059 58.23828 57.38617 56.74749 58.34351 59.16644 57.05620
[17] 59.84411 56.29042 56.32422 53.27021
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] NA 69.90239 69.73299 70.94464 70.55756 70.45801 68.19547 69.93804
[9] 72.57970 68.68901
> rowSums(tmp5)
[1] NA 1398.048 1394.660 1418.893 1411.151 1409.160 1363.909 1398.761
[9] 1451.594 1373.780
> rowVars(tmp5)
[1] 53.37529 58.67766 87.47355 69.72406 57.42052 81.92032 83.79517 68.58403
[9] 55.90186 68.85265
> rowSd(tmp5)
[1] 7.305839 7.660134 9.352729 8.350093 7.577633 9.050984 9.153970 8.281548
[9] 7.476755 8.297749
> rowMax(tmp5)
[1] NA 88.73694 92.30858 89.60406 85.34730 85.15058 82.21749 81.58454
[9] 83.24788 87.89538
> rowMin(tmp5)
[1] NA 59.15026 53.27021 55.98912 58.23828 53.02462 54.30289 56.32422
[9] 57.05620 56.32756
>
> colMeans(tmp5)
[1] NA 71.50616 69.79455 70.88571 65.12370 70.59601 73.59373 68.64865
[9] 71.11299 69.78600 68.10343 68.69846 72.40651 69.87817 70.51680 70.52389
[17] 72.24608 70.43260 70.01880 71.89744
> colSums(tmp5)
[1] NA 715.0616 697.9455 708.8571 651.2370 705.9601 735.9373 686.4865
[9] 711.1299 697.8600 681.0343 686.9846 724.0651 698.7817 705.1680 705.2389
[17] 722.4608 704.3260 700.1880 718.9744
> colVars(tmp5)
[1] NA 78.89909 32.52788 81.46703 47.72819 55.29288 64.41836
[8] 99.30827 74.90775 99.19606 56.91248 72.00642 81.98567 69.52301
[15] 76.84670 54.35125 66.47295 88.61340 42.90383 107.00971
> colSd(tmp5)
[1] NA 8.882516 5.703322 9.025909 6.908559 7.435919 8.026105
[8] 9.965353 8.654926 9.959722 7.544036 8.485660 9.054594 8.338046
[15] 8.766225 7.372330 8.153094 9.413469 6.550101 10.344550
> colMax(tmp5)
[1] NA 83.30777 76.60757 84.57572 76.01868 78.86156 92.30858 85.34730
[9] 83.43183 83.56569 83.24788 81.32268 88.73694 87.89538 82.77274 81.28790
[17] 84.89429 85.15058 77.43920 89.60406
> colMin(tmp5)
[1] NA 56.32756 58.20990 60.22324 54.30289 59.07029 62.04375 53.02462
[9] 58.30325 55.50059 58.23828 57.38617 56.74749 58.34351 59.16644 57.05620
[17] 59.84411 56.29042 56.32422 53.27021
>
> Max(tmp5,na.rm=TRUE)
[1] 92.30858
> Min(tmp5,na.rm=TRUE)
[1] 53.02462
> mean(tmp5,na.rm=TRUE)
[1] 70.25792
> Sum(tmp5,na.rm=TRUE)
[1] 13981.33
> Var(tmp5,na.rm=TRUE)
[1] 67.05306
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 71.65104 69.90239 69.73299 70.94464 70.55756 70.45801 68.19547 69.93804
[9] 72.57970 68.68901
> rowSums(tmp5,na.rm=TRUE)
[1] 1361.370 1398.048 1394.660 1418.893 1411.151 1409.160 1363.909 1398.761
[9] 1451.594 1373.780
> rowVars(tmp5,na.rm=TRUE)
[1] 53.37529 58.67766 87.47355 69.72406 57.42052 81.92032 83.79517 68.58403
[9] 55.90186 68.85265
> rowSd(tmp5,na.rm=TRUE)
[1] 7.305839 7.660134 9.352729 8.350093 7.577633 9.050984 9.153970 8.281548
[9] 7.476755 8.297749
> rowMax(tmp5,na.rm=TRUE)
[1] 84.89429 88.73694 92.30858 89.60406 85.34730 85.15058 82.21749 81.58454
[9] 83.24788 87.89538
> rowMin(tmp5,na.rm=TRUE)
[1] 57.38617 59.15026 53.27021 55.98912 58.23828 53.02462 54.30289 56.32422
[9] 57.05620 56.32756
>
> colMeans(tmp5,na.rm=TRUE)
[1] 69.29212 71.50616 69.79455 70.88571 65.12370 70.59601 73.59373 68.64865
[9] 71.11299 69.78600 68.10343 68.69846 72.40651 69.87817 70.51680 70.52389
[17] 72.24608 70.43260 70.01880 71.89744
> colSums(tmp5,na.rm=TRUE)
[1] 623.6290 715.0616 697.9455 708.8571 651.2370 705.9601 735.9373 686.4865
[9] 711.1299 697.8600 681.0343 686.9846 724.0651 698.7817 705.1680 705.2389
[17] 722.4608 704.3260 700.1880 718.9744
> colVars(tmp5,na.rm=TRUE)
[1] 61.83000 78.89909 32.52788 81.46703 47.72819 55.29288 64.41836
[8] 99.30827 74.90775 99.19606 56.91248 72.00642 81.98567 69.52301
[15] 76.84670 54.35125 66.47295 88.61340 42.90383 107.00971
> colSd(tmp5,na.rm=TRUE)
[1] 7.863205 8.882516 5.703322 9.025909 6.908559 7.435919 8.026105
[8] 9.965353 8.654926 9.959722 7.544036 8.485660 9.054594 8.338046
[15] 8.766225 7.372330 8.153094 9.413469 6.550101 10.344550
> colMax(tmp5,na.rm=TRUE)
[1] 82.21749 83.30777 76.60757 84.57572 76.01868 78.86156 92.30858 85.34730
[9] 83.43183 83.56569 83.24788 81.32268 88.73694 87.89538 82.77274 81.28790
[17] 84.89429 85.15058 77.43920 89.60406
> colMin(tmp5,na.rm=TRUE)
[1] 59.15026 56.32756 58.20990 60.22324 54.30289 59.07029 62.04375 53.02462
[9] 58.30325 55.50059 58.23828 57.38617 56.74749 58.34351 59.16644 57.05620
[17] 59.84411 56.29042 56.32422 53.27021
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] NaN 69.90239 69.73299 70.94464 70.55756 70.45801 68.19547 69.93804
[9] 72.57970 68.68901
> rowSums(tmp5,na.rm=TRUE)
[1] 0.000 1398.048 1394.660 1418.893 1411.151 1409.160 1363.909 1398.761
[9] 1451.594 1373.780
> rowVars(tmp5,na.rm=TRUE)
[1] NA 58.67766 87.47355 69.72406 57.42052 81.92032 83.79517 68.58403
[9] 55.90186 68.85265
> rowSd(tmp5,na.rm=TRUE)
[1] NA 7.660134 9.352729 8.350093 7.577633 9.050984 9.153970 8.281548
[9] 7.476755 8.297749
> rowMax(tmp5,na.rm=TRUE)
[1] NA 88.73694 92.30858 89.60406 85.34730 85.15058 82.21749 81.58454
[9] 83.24788 87.89538
> rowMin(tmp5,na.rm=TRUE)
[1] NA 59.15026 53.27021 55.98912 58.23828 53.02462 54.30289 56.32422
[9] 57.05620 56.32756
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] NaN 70.75801 69.15582 70.96830 64.43491 70.15211 73.79322 68.05909
[9] 72.53630 69.48981 67.05312 69.95538 72.29848 70.80431 69.26288 70.74323
[17] 70.84073 70.91627 69.28504 72.41824
> colSums(tmp5,na.rm=TRUE)
[1] 0.0000 636.8221 622.4024 638.7147 579.9142 631.3690 664.1390 612.5318
[9] 652.8267 625.4083 603.4781 629.5984 650.6864 637.2388 623.3660 636.6891
[17] 637.5665 638.2464 623.5654 651.7641
> colVars(tmp5,na.rm=TRUE)
[1] NA 82.46452 32.00423 91.57368 48.35673 59.98779 72.02292
[8] 107.81146 61.48099 110.60863 51.61602 63.23390 92.10259 68.56376
[15] 68.76420 60.60393 52.56301 97.05837 42.20975 117.33466
> colSd(tmp5,na.rm=TRUE)
[1] NA 9.080998 5.657228 9.569414 6.953900 7.745179 8.486632
[8] 10.383230 7.840982 10.517064 7.184429 7.951975 9.597010 8.280324
[15] 8.292418 7.784853 7.250035 9.851821 6.496903 10.832112
> colMax(tmp5,na.rm=TRUE)
[1] -Inf 83.30777 76.60757 84.57572 76.01868 78.86156 92.30858 85.34730
[9] 83.43183 83.56569 83.24788 81.32268 88.73694 87.89538 82.77274 81.28790
[17] 80.74823 85.15058 77.43920 89.60406
> colMin(tmp5,na.rm=TRUE)
[1] Inf 56.32756 58.20990 60.22324 54.30289 59.07029 62.04375 53.02462
[9] 60.62948 55.50059 58.23828 57.83956 56.74749 58.34351 59.16644 57.05620
[17] 59.84411 56.29042 56.32422 53.27021
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 231.2041 329.6620 126.9070 173.3150 306.4118 224.8073 279.9158 194.1987
[9] 165.0642 232.1596
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 231.2041 329.6620 126.9070 173.3150 306.4118 224.8073 279.9158 194.1987
[9] 165.0642 232.1596
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -2.842171e-14 -5.684342e-14 -5.684342e-14 -8.526513e-14 1.989520e-13
[6] -1.705303e-13 -2.131628e-13 2.842171e-14 1.421085e-13 8.526513e-14
[11] -5.684342e-14 -2.842171e-14 -7.105427e-14 -3.410605e-13 1.421085e-14
[16] -1.705303e-13 -5.684342e-14 -1.136868e-13 0.000000e+00 -2.273737e-13
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
5 7
9 9
10 6
5 5
4 2
1 19
2 8
5 18
3 20
7 7
10 16
9 4
10 5
9 8
2 9
2 5
10 14
8 18
4 18
10 17
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.176353
> Min(tmp)
[1] -3.268377
> mean(tmp)
[1] 0.04627426
> Sum(tmp)
[1] 4.627426
> Var(tmp)
[1] 0.9800545
>
> rowMeans(tmp)
[1] 0.04627426
> rowSums(tmp)
[1] 4.627426
> rowVars(tmp)
[1] 0.9800545
> rowSd(tmp)
[1] 0.989977
> rowMax(tmp)
[1] 2.176353
> rowMin(tmp)
[1] -3.268377
>
> colMeans(tmp)
[1] -0.090723337 0.204877538 1.143364250 0.997712857 -0.791250413
[6] 1.651240683 -0.037137952 -0.884029410 -0.295992945 -0.003852997
[11] -1.119510840 -0.159578986 0.858113867 -0.332351401 0.902035205
[16] 1.341531591 0.091949869 0.106649330 1.229844218 -0.988284456
[21] -1.044085100 0.285258862 0.358206000 2.073543570 0.398453240
[26] -1.753413424 0.015208426 -0.725126213 0.338238728 -1.027357465
[31] -1.940644507 -0.118714827 0.492142931 -0.296743191 -0.022179604
[36] -1.994324764 0.126763224 0.110486745 1.039712222 -0.237050819
[41] -0.603575407 0.248007227 1.581933161 -0.290669723 0.128701332
[46] -1.271822881 1.470813043 -0.209099319 -1.761169252 1.360211764
[51] -0.269204889 0.502557954 1.715591990 -0.938735877 0.827318367
[56] -1.085047238 -0.261123515 -3.268377297 -0.360517880 0.797091258
[61] 1.130829307 0.241432589 -1.071402790 2.176352991 0.182644502
[66] 1.531126908 0.255378460 -0.348982970 -1.763634251 -0.009733883
[71] -2.004285960 1.013022457 -0.376287893 -0.378265682 -0.114897848
[76] 0.452567266 1.891512407 0.383800672 0.585047278 -1.084257830
[81] 1.304211845 0.809796747 0.414345456 0.100111715 0.436706471
[86] 0.781121990 -0.156370255 -1.296774555 -0.008131533 -0.562229193
[91] 0.636037301 -0.391002490 0.873157654 -1.223613975 -0.236222426
[96] 1.210765986 0.560734564 0.437950214 -0.436845851 0.465846744
> colSums(tmp)
[1] -0.090723337 0.204877538 1.143364250 0.997712857 -0.791250413
[6] 1.651240683 -0.037137952 -0.884029410 -0.295992945 -0.003852997
[11] -1.119510840 -0.159578986 0.858113867 -0.332351401 0.902035205
[16] 1.341531591 0.091949869 0.106649330 1.229844218 -0.988284456
[21] -1.044085100 0.285258862 0.358206000 2.073543570 0.398453240
[26] -1.753413424 0.015208426 -0.725126213 0.338238728 -1.027357465
[31] -1.940644507 -0.118714827 0.492142931 -0.296743191 -0.022179604
[36] -1.994324764 0.126763224 0.110486745 1.039712222 -0.237050819
[41] -0.603575407 0.248007227 1.581933161 -0.290669723 0.128701332
[46] -1.271822881 1.470813043 -0.209099319 -1.761169252 1.360211764
[51] -0.269204889 0.502557954 1.715591990 -0.938735877 0.827318367
[56] -1.085047238 -0.261123515 -3.268377297 -0.360517880 0.797091258
[61] 1.130829307 0.241432589 -1.071402790 2.176352991 0.182644502
[66] 1.531126908 0.255378460 -0.348982970 -1.763634251 -0.009733883
[71] -2.004285960 1.013022457 -0.376287893 -0.378265682 -0.114897848
[76] 0.452567266 1.891512407 0.383800672 0.585047278 -1.084257830
[81] 1.304211845 0.809796747 0.414345456 0.100111715 0.436706471
[86] 0.781121990 -0.156370255 -1.296774555 -0.008131533 -0.562229193
[91] 0.636037301 -0.391002490 0.873157654 -1.223613975 -0.236222426
[96] 1.210765986 0.560734564 0.437950214 -0.436845851 0.465846744
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -0.090723337 0.204877538 1.143364250 0.997712857 -0.791250413
[6] 1.651240683 -0.037137952 -0.884029410 -0.295992945 -0.003852997
[11] -1.119510840 -0.159578986 0.858113867 -0.332351401 0.902035205
[16] 1.341531591 0.091949869 0.106649330 1.229844218 -0.988284456
[21] -1.044085100 0.285258862 0.358206000 2.073543570 0.398453240
[26] -1.753413424 0.015208426 -0.725126213 0.338238728 -1.027357465
[31] -1.940644507 -0.118714827 0.492142931 -0.296743191 -0.022179604
[36] -1.994324764 0.126763224 0.110486745 1.039712222 -0.237050819
[41] -0.603575407 0.248007227 1.581933161 -0.290669723 0.128701332
[46] -1.271822881 1.470813043 -0.209099319 -1.761169252 1.360211764
[51] -0.269204889 0.502557954 1.715591990 -0.938735877 0.827318367
[56] -1.085047238 -0.261123515 -3.268377297 -0.360517880 0.797091258
[61] 1.130829307 0.241432589 -1.071402790 2.176352991 0.182644502
[66] 1.531126908 0.255378460 -0.348982970 -1.763634251 -0.009733883
[71] -2.004285960 1.013022457 -0.376287893 -0.378265682 -0.114897848
[76] 0.452567266 1.891512407 0.383800672 0.585047278 -1.084257830
[81] 1.304211845 0.809796747 0.414345456 0.100111715 0.436706471
[86] 0.781121990 -0.156370255 -1.296774555 -0.008131533 -0.562229193
[91] 0.636037301 -0.391002490 0.873157654 -1.223613975 -0.236222426
[96] 1.210765986 0.560734564 0.437950214 -0.436845851 0.465846744
> colMin(tmp)
[1] -0.090723337 0.204877538 1.143364250 0.997712857 -0.791250413
[6] 1.651240683 -0.037137952 -0.884029410 -0.295992945 -0.003852997
[11] -1.119510840 -0.159578986 0.858113867 -0.332351401 0.902035205
[16] 1.341531591 0.091949869 0.106649330 1.229844218 -0.988284456
[21] -1.044085100 0.285258862 0.358206000 2.073543570 0.398453240
[26] -1.753413424 0.015208426 -0.725126213 0.338238728 -1.027357465
[31] -1.940644507 -0.118714827 0.492142931 -0.296743191 -0.022179604
[36] -1.994324764 0.126763224 0.110486745 1.039712222 -0.237050819
[41] -0.603575407 0.248007227 1.581933161 -0.290669723 0.128701332
[46] -1.271822881 1.470813043 -0.209099319 -1.761169252 1.360211764
[51] -0.269204889 0.502557954 1.715591990 -0.938735877 0.827318367
[56] -1.085047238 -0.261123515 -3.268377297 -0.360517880 0.797091258
[61] 1.130829307 0.241432589 -1.071402790 2.176352991 0.182644502
[66] 1.531126908 0.255378460 -0.348982970 -1.763634251 -0.009733883
[71] -2.004285960 1.013022457 -0.376287893 -0.378265682 -0.114897848
[76] 0.452567266 1.891512407 0.383800672 0.585047278 -1.084257830
[81] 1.304211845 0.809796747 0.414345456 0.100111715 0.436706471
[86] 0.781121990 -0.156370255 -1.296774555 -0.008131533 -0.562229193
[91] 0.636037301 -0.391002490 0.873157654 -1.223613975 -0.236222426
[96] 1.210765986 0.560734564 0.437950214 -0.436845851 0.465846744
> colMedians(tmp)
[1] -0.090723337 0.204877538 1.143364250 0.997712857 -0.791250413
[6] 1.651240683 -0.037137952 -0.884029410 -0.295992945 -0.003852997
[11] -1.119510840 -0.159578986 0.858113867 -0.332351401 0.902035205
[16] 1.341531591 0.091949869 0.106649330 1.229844218 -0.988284456
[21] -1.044085100 0.285258862 0.358206000 2.073543570 0.398453240
[26] -1.753413424 0.015208426 -0.725126213 0.338238728 -1.027357465
[31] -1.940644507 -0.118714827 0.492142931 -0.296743191 -0.022179604
[36] -1.994324764 0.126763224 0.110486745 1.039712222 -0.237050819
[41] -0.603575407 0.248007227 1.581933161 -0.290669723 0.128701332
[46] -1.271822881 1.470813043 -0.209099319 -1.761169252 1.360211764
[51] -0.269204889 0.502557954 1.715591990 -0.938735877 0.827318367
[56] -1.085047238 -0.261123515 -3.268377297 -0.360517880 0.797091258
[61] 1.130829307 0.241432589 -1.071402790 2.176352991 0.182644502
[66] 1.531126908 0.255378460 -0.348982970 -1.763634251 -0.009733883
[71] -2.004285960 1.013022457 -0.376287893 -0.378265682 -0.114897848
[76] 0.452567266 1.891512407 0.383800672 0.585047278 -1.084257830
[81] 1.304211845 0.809796747 0.414345456 0.100111715 0.436706471
[86] 0.781121990 -0.156370255 -1.296774555 -0.008131533 -0.562229193
[91] 0.636037301 -0.391002490 0.873157654 -1.223613975 -0.236222426
[96] 1.210765986 0.560734564 0.437950214 -0.436845851 0.465846744
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.09072334 0.2048775 1.143364 0.9977129 -0.7912504 1.651241 -0.03713795
[2,] -0.09072334 0.2048775 1.143364 0.9977129 -0.7912504 1.651241 -0.03713795
[,8] [,9] [,10] [,11] [,12] [,13]
[1,] -0.8840294 -0.2959929 -0.003852997 -1.119511 -0.159579 0.8581139
[2,] -0.8840294 -0.2959929 -0.003852997 -1.119511 -0.159579 0.8581139
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] -0.3323514 0.9020352 1.341532 0.09194987 0.1066493 1.229844 -0.9882845
[2,] -0.3323514 0.9020352 1.341532 0.09194987 0.1066493 1.229844 -0.9882845
[,21] [,22] [,23] [,24] [,25] [,26] [,27]
[1,] -1.044085 0.2852589 0.358206 2.073544 0.3984532 -1.753413 0.01520843
[2,] -1.044085 0.2852589 0.358206 2.073544 0.3984532 -1.753413 0.01520843
[,28] [,29] [,30] [,31] [,32] [,33] [,34]
[1,] -0.7251262 0.3382387 -1.027357 -1.940645 -0.1187148 0.4921429 -0.2967432
[2,] -0.7251262 0.3382387 -1.027357 -1.940645 -0.1187148 0.4921429 -0.2967432
[,35] [,36] [,37] [,38] [,39] [,40] [,41]
[1,] -0.0221796 -1.994325 0.1267632 0.1104867 1.039712 -0.2370508 -0.6035754
[2,] -0.0221796 -1.994325 0.1267632 0.1104867 1.039712 -0.2370508 -0.6035754
[,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 0.2480072 1.581933 -0.2906697 0.1287013 -1.271823 1.470813 -0.2090993
[2,] 0.2480072 1.581933 -0.2906697 0.1287013 -1.271823 1.470813 -0.2090993
[,49] [,50] [,51] [,52] [,53] [,54] [,55]
[1,] -1.761169 1.360212 -0.2692049 0.502558 1.715592 -0.9387359 0.8273184
[2,] -1.761169 1.360212 -0.2692049 0.502558 1.715592 -0.9387359 0.8273184
[,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] -1.085047 -0.2611235 -3.268377 -0.3605179 0.7970913 1.130829 0.2414326
[2,] -1.085047 -0.2611235 -3.268377 -0.3605179 0.7970913 1.130829 0.2414326
[,63] [,64] [,65] [,66] [,67] [,68] [,69]
[1,] -1.071403 2.176353 0.1826445 1.531127 0.2553785 -0.348983 -1.763634
[2,] -1.071403 2.176353 0.1826445 1.531127 0.2553785 -0.348983 -1.763634
[,70] [,71] [,72] [,73] [,74] [,75] [,76]
[1,] -0.009733883 -2.004286 1.013022 -0.3762879 -0.3782657 -0.1148978 0.4525673
[2,] -0.009733883 -2.004286 1.013022 -0.3762879 -0.3782657 -0.1148978 0.4525673
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] 1.891512 0.3838007 0.5850473 -1.084258 1.304212 0.8097967 0.4143455
[2,] 1.891512 0.3838007 0.5850473 -1.084258 1.304212 0.8097967 0.4143455
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] 0.1001117 0.4367065 0.781122 -0.1563703 -1.296775 -0.008131533 -0.5622292
[2,] 0.1001117 0.4367065 0.781122 -0.1563703 -1.296775 -0.008131533 -0.5622292
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] 0.6360373 -0.3910025 0.8731577 -1.223614 -0.2362224 1.210766 0.5607346
[2,] 0.6360373 -0.3910025 0.8731577 -1.223614 -0.2362224 1.210766 0.5607346
[,98] [,99] [,100]
[1,] 0.4379502 -0.4368459 0.4658467
[2,] 0.4379502 -0.4368459 0.4658467
>
>
> Max(tmp2)
[1] 2.745916
> Min(tmp2)
[1] -2.550784
> mean(tmp2)
[1] -0.128027
> Sum(tmp2)
[1] -12.8027
> Var(tmp2)
[1] 1.094301
>
> rowMeans(tmp2)
[1] 2.07902908 0.56174119 2.16004870 0.38865108 0.71710085 0.15747765
[7] 0.99124326 1.65599851 1.37139379 -1.07703086 -2.55078439 -1.07709026
[13] 0.25639103 1.42367645 -0.60272912 -0.89281195 -0.51371819 -0.95979526
[19] -2.47862526 2.30743606 -0.95005211 1.37593337 0.44460191 -1.52102948
[25] -1.13720014 -0.24854189 -1.04621226 -0.68839903 0.52472168 -1.00338353
[31] -0.40317453 -1.01172503 0.56348499 0.05080943 -0.50189570 -0.81048565
[37] -0.55802398 -2.22772196 -1.96244689 1.00864805 0.33439784 0.68315145
[43] -0.35605206 0.93684282 -0.54189262 0.08047483 -1.09874765 -0.54946980
[49] 0.93012130 -1.40409131 -0.70744971 -0.32931654 -0.95184734 -0.88102303
[55] 0.26869024 -0.62921097 -0.57094455 0.44582992 2.74591559 -1.28185672
[61] -0.59526787 -0.44190537 -0.27219934 -1.88543926 -0.93568572 1.59351609
[67] -1.93828641 0.85408369 -0.48822218 0.14787633 -0.23288860 -0.53145045
[73] -0.53721251 -0.16581793 -0.29973006 0.27418627 1.67824042 0.43650659
[79] 1.01125212 -0.19661155 0.25523438 0.71779101 -0.68223037 0.43789706
[85] 1.22592371 -0.43091255 -0.38866467 0.15131805 -0.09360314 -1.02829439
[91] -0.53760760 -0.66268908 0.60778341 -0.86705959 0.23091341 -1.36555774
[97] -1.25381945 1.09917625 0.65961206 0.70811120
> rowSums(tmp2)
[1] 2.07902908 0.56174119 2.16004870 0.38865108 0.71710085 0.15747765
[7] 0.99124326 1.65599851 1.37139379 -1.07703086 -2.55078439 -1.07709026
[13] 0.25639103 1.42367645 -0.60272912 -0.89281195 -0.51371819 -0.95979526
[19] -2.47862526 2.30743606 -0.95005211 1.37593337 0.44460191 -1.52102948
[25] -1.13720014 -0.24854189 -1.04621226 -0.68839903 0.52472168 -1.00338353
[31] -0.40317453 -1.01172503 0.56348499 0.05080943 -0.50189570 -0.81048565
[37] -0.55802398 -2.22772196 -1.96244689 1.00864805 0.33439784 0.68315145
[43] -0.35605206 0.93684282 -0.54189262 0.08047483 -1.09874765 -0.54946980
[49] 0.93012130 -1.40409131 -0.70744971 -0.32931654 -0.95184734 -0.88102303
[55] 0.26869024 -0.62921097 -0.57094455 0.44582992 2.74591559 -1.28185672
[61] -0.59526787 -0.44190537 -0.27219934 -1.88543926 -0.93568572 1.59351609
[67] -1.93828641 0.85408369 -0.48822218 0.14787633 -0.23288860 -0.53145045
[73] -0.53721251 -0.16581793 -0.29973006 0.27418627 1.67824042 0.43650659
[79] 1.01125212 -0.19661155 0.25523438 0.71779101 -0.68223037 0.43789706
[85] 1.22592371 -0.43091255 -0.38866467 0.15131805 -0.09360314 -1.02829439
[91] -0.53760760 -0.66268908 0.60778341 -0.86705959 0.23091341 -1.36555774
[97] -1.25381945 1.09917625 0.65961206 0.70811120
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 2.07902908 0.56174119 2.16004870 0.38865108 0.71710085 0.15747765
[7] 0.99124326 1.65599851 1.37139379 -1.07703086 -2.55078439 -1.07709026
[13] 0.25639103 1.42367645 -0.60272912 -0.89281195 -0.51371819 -0.95979526
[19] -2.47862526 2.30743606 -0.95005211 1.37593337 0.44460191 -1.52102948
[25] -1.13720014 -0.24854189 -1.04621226 -0.68839903 0.52472168 -1.00338353
[31] -0.40317453 -1.01172503 0.56348499 0.05080943 -0.50189570 -0.81048565
[37] -0.55802398 -2.22772196 -1.96244689 1.00864805 0.33439784 0.68315145
[43] -0.35605206 0.93684282 -0.54189262 0.08047483 -1.09874765 -0.54946980
[49] 0.93012130 -1.40409131 -0.70744971 -0.32931654 -0.95184734 -0.88102303
[55] 0.26869024 -0.62921097 -0.57094455 0.44582992 2.74591559 -1.28185672
[61] -0.59526787 -0.44190537 -0.27219934 -1.88543926 -0.93568572 1.59351609
[67] -1.93828641 0.85408369 -0.48822218 0.14787633 -0.23288860 -0.53145045
[73] -0.53721251 -0.16581793 -0.29973006 0.27418627 1.67824042 0.43650659
[79] 1.01125212 -0.19661155 0.25523438 0.71779101 -0.68223037 0.43789706
[85] 1.22592371 -0.43091255 -0.38866467 0.15131805 -0.09360314 -1.02829439
[91] -0.53760760 -0.66268908 0.60778341 -0.86705959 0.23091341 -1.36555774
[97] -1.25381945 1.09917625 0.65961206 0.70811120
> rowMin(tmp2)
[1] 2.07902908 0.56174119 2.16004870 0.38865108 0.71710085 0.15747765
[7] 0.99124326 1.65599851 1.37139379 -1.07703086 -2.55078439 -1.07709026
[13] 0.25639103 1.42367645 -0.60272912 -0.89281195 -0.51371819 -0.95979526
[19] -2.47862526 2.30743606 -0.95005211 1.37593337 0.44460191 -1.52102948
[25] -1.13720014 -0.24854189 -1.04621226 -0.68839903 0.52472168 -1.00338353
[31] -0.40317453 -1.01172503 0.56348499 0.05080943 -0.50189570 -0.81048565
[37] -0.55802398 -2.22772196 -1.96244689 1.00864805 0.33439784 0.68315145
[43] -0.35605206 0.93684282 -0.54189262 0.08047483 -1.09874765 -0.54946980
[49] 0.93012130 -1.40409131 -0.70744971 -0.32931654 -0.95184734 -0.88102303
[55] 0.26869024 -0.62921097 -0.57094455 0.44582992 2.74591559 -1.28185672
[61] -0.59526787 -0.44190537 -0.27219934 -1.88543926 -0.93568572 1.59351609
[67] -1.93828641 0.85408369 -0.48822218 0.14787633 -0.23288860 -0.53145045
[73] -0.53721251 -0.16581793 -0.29973006 0.27418627 1.67824042 0.43650659
[79] 1.01125212 -0.19661155 0.25523438 0.71779101 -0.68223037 0.43789706
[85] 1.22592371 -0.43091255 -0.38866467 0.15131805 -0.09360314 -1.02829439
[91] -0.53760760 -0.66268908 0.60778341 -0.86705959 0.23091341 -1.36555774
[97] -1.25381945 1.09917625 0.65961206 0.70811120
>
> colMeans(tmp2)
[1] -0.128027
> colSums(tmp2)
[1] -12.8027
> colVars(tmp2)
[1] 1.094301
> colSd(tmp2)
[1] 1.046089
> colMax(tmp2)
[1] 2.745916
> colMin(tmp2)
[1] -2.550784
> colMedians(tmp2)
[1] -0.3145233
> colRanges(tmp2)
[,1]
[1,] -2.550784
[2,] 2.745916
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -3.3548951 2.9077472 -2.6423437 1.7978963 -0.1347771 0.0268736
[7] 4.3442711 -1.8002008 3.2119279 1.5046002
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.7515836
[2,] -1.2744420
[3,] -0.2345374
[4,] 0.2952030
[5,] 1.5588559
>
> rowApply(tmp,sum)
[1] 3.7908300 -2.0018384 4.9735800 1.3142133 -1.5672813 -0.4253261
[7] -1.2565787 -0.5359954 -0.3652973 1.9347937
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 8 8 3 1 3 4 8 1 2 9
[2,] 10 2 8 10 9 2 2 9 6 2
[3,] 1 6 4 4 2 6 7 7 4 4
[4,] 4 9 10 6 4 9 5 10 3 6
[5,] 7 4 2 2 6 5 10 5 5 7
[6,] 5 7 5 9 5 1 3 8 1 10
[7,] 3 5 9 8 7 3 6 6 9 8
[8,] 6 1 1 7 8 8 4 3 7 1
[9,] 2 3 6 5 10 7 9 4 8 3
[10,] 9 10 7 3 1 10 1 2 10 5
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.4120318 -1.9266539 -3.0261684 -1.6943031 -0.5520461 -0.4493792
[7] 1.8339990 -4.5931764 2.3492289 1.3206100 1.3022670 -2.5092850
[13] -0.6084488 0.1604670 2.2234019 -0.2897372 -4.7302321 -0.4043329
[19] -0.3141137 1.7487962
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.7436980
[2,] -0.2590457
[3,] 0.2692601
[4,] 0.5593639
[5,] 0.5861515
>
> rowApply(tmp,sum)
[1] -11.924341 -1.856646 6.426771 -5.319012 2.926153
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 10 12 11 17 15
[2,] 13 11 15 3 3
[3,] 11 6 3 5 9
[4,] 2 7 20 6 5
[5,] 8 10 12 2 19
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.7436980 -0.2263915 -0.72979955 -1.8436969 -0.9627755 -1.3537984
[2,] -0.2590457 -0.4221988 -0.66632184 -0.6404421 -0.4525203 -0.5070030
[3,] 0.2692601 0.9846897 -0.53476160 2.4476147 0.3627510 -0.3626058
[4,] 0.5593639 -1.1321783 -1.07936451 -1.0705258 -1.6193516 1.8220908
[5,] 0.5861515 -1.1305750 -0.01592088 -0.5872530 2.1198503 -0.0480628
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.9215772 -1.4867368 -0.19477971 -0.3084331 0.7826490 1.1269363
[2,] 0.1441994 -0.5847340 -0.04117836 -1.0933093 1.4373829 -0.1508847
[3,] 0.4822197 0.7135785 1.23895136 1.4286948 -0.2798853 -1.6053906
[4,] -0.1563572 -3.3552868 1.39553976 0.4679424 -0.1698365 -1.1021501
[5,] 0.4423599 0.1200028 -0.04930418 0.8257153 -0.4680430 -0.7777959
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.24173506 -2.4404679 0.52176776 -0.8705581 -1.50019893 -1.8261596
[2,] -1.27335241 2.6262974 1.77015584 -1.3292679 0.02943634 1.5392732
[3,] 0.04922986 -0.5107423 -0.09129066 -0.1205063 -1.76923222 0.1876032
[4,] 0.01908555 -0.2364762 0.03159761 -0.1825115 -0.31583489 -0.5158542
[5,] 0.35485319 0.7218560 -0.00882862 2.2131065 -1.17440243 0.2108046
[,19] [,20]
[1,] -1.119984 0.08847155
[2,] -1.216577 -0.76655523
[3,] 2.038762 1.49783064
[4,] 1.149372 0.17172395
[5,] -1.165687 0.75732528
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 624 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 543 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 -1.461567 1.442306 -0.1844367 -0.6753881 -0.05446495 -1.826612 0.1230951
col8 col9 col10 col11 col12 col13 col14
row1 -1.647105 -0.756616 -1.30385 -0.8640069 -0.3357482 0.2617637 -1.841947
col15 col16 col17 col18 col19 col20
row1 -0.7685515 0.1567848 0.000484904 -0.3360629 -0.5546109 0.2335957
> tmp[,"col10"]
col10
row1 -1.3038501
row2 -0.1086450
row3 -0.6728907
row4 0.5017439
row5 -1.3795073
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -1.461567 1.442306 -0.1844367 -0.6753881 -0.05446495 -1.8266122 0.1230951
row5 0.421360 1.412225 -1.8541977 -0.4416365 0.22737327 0.2133497 1.1689789
col8 col9 col10 col11 col12 col13 col14
row1 -1.6471047 -0.756616 -1.303850 -0.8640069 -0.3357482 0.2617637 -1.841947
row5 0.3158185 -0.133859 -1.379507 -1.1779379 -0.9852829 -2.8874185 -2.670699
col15 col16 col17 col18 col19 col20
row1 -0.768551482 0.1567848 0.000484904 -0.3360629 -0.5546109 0.2335957
row5 0.006858665 0.5033668 0.677140128 -0.5993274 0.4554286 1.1873880
> tmp[,c("col6","col20")]
col6 col20
row1 -1.8266122 0.23359566
row2 0.9688276 -0.49088081
row3 -0.9297702 1.29073830
row4 -0.2567671 -0.02323868
row5 0.2133497 1.18738804
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.8266122 0.2335957
row5 0.2133497 1.1873880
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.04527 48.90174 51.72462 47.9559 49.65989 107.0109 48.87439 49.44602
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.54169 52.0285 50.90914 51.67146 50.79819 48.96218 50.06577 51.31393
col17 col18 col19 col20
row1 49.64026 49.54687 49.76956 105.9395
> tmp[,"col10"]
col10
row1 52.02850
row2 30.60456
row3 30.22374
row4 29.61892
row5 50.02148
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.04527 48.90174 51.72462 47.95590 49.65989 107.0109 48.87439 49.44602
row5 49.02776 48.76149 49.24390 49.02281 49.80739 102.7006 49.29621 50.57358
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.54169 52.02850 50.90914 51.67146 50.79819 48.96218 50.06577 51.31393
row5 49.64234 50.02148 50.27100 49.57961 48.68607 48.84103 48.18389 49.34856
col17 col18 col19 col20
row1 49.64026 49.54687 49.76956 105.9395
row5 50.58914 49.51427 48.83641 105.9311
> tmp[,c("col6","col20")]
col6 col20
row1 107.01093 105.93946
row2 74.99596 76.55213
row3 75.53868 73.97589
row4 75.59485 76.58713
row5 102.70060 105.93114
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 107.0109 105.9395
row5 102.7006 105.9311
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 107.0109 105.9395
row5 102.7006 105.9311
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.8774821
[2,] 0.4405534
[3,] -0.7859441
[4,] 0.4270749
[5,] -1.7003735
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.6701610 0.6339371
[2,] -0.1435779 1.0472998
[3,] 2.2428444 -2.1470644
[4,] 1.4821399 -0.9627847
[5,] -0.8015051 1.2126704
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -1.0603159 -0.05258727
[2,] 0.8199094 -1.04961632
[3,] -0.4441452 1.08387398
[4,] -0.1131516 -0.20930448
[5,] 0.9217924 1.10436560
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -1.060316
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -1.0603159
[2,] 0.8199094
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 0.3798746 0.2471807 -1.188012 -1.111802 -0.3541126 1.096140 -0.4460141
row1 0.5444476 -0.5970879 1.589119 -1.109343 -0.4586308 1.952988 0.1205747
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.06419481 -0.008859637 -1.0204021 -0.96519427 -1.069629 -2.3308326
row1 -1.42334927 -0.797898128 -0.9443915 -0.08642845 0.997603 0.7186506
[,14] [,15] [,16] [,17] [,18] [,19]
row3 -0.07378381 0.1164671 -0.9584683 0.09039053 1.4098381 1.594847611
row1 0.23246371 1.9563041 0.7505478 0.56997142 0.9497657 0.003491192
[,20]
row3 0.3905983
row1 1.0139081
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.1736785 0.7449902 0.2155801 0.04340018 -1.675289 0.5597072 2.483455
[,8] [,9] [,10]
row2 -0.4376478 1.40628 -2.081108
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -1.157501 0.5818541 -0.7538188 -0.8014265 1.509608 -1.948772 -0.9879128
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -1.967571 -0.4499711 0.5233345 -2.964678 1.836942 -1.110311 -1.002638
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.9766278 -0.8419015 -0.2858836 0.5249566 -0.6850887 0.7237888
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x000001d306cfdcb0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM53946e6faf0"
[2] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM539449344685"
[3] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM5394be912a8"
[4] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM5394cd8796c"
[5] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM53944ef53679"
[6] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM539459c16bde"
[7] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM539465593e66"
[8] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM539423f41d9b"
[9] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM53947c5e5cdf"
[10] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM5394652e2e3d"
[11] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM53944ec954e7"
[12] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM53943a785479"
[13] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM53944f0d4b76"
[14] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM53947ffa5aa2"
[15] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM539441bf481c"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x000001d3093ff7d0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x000001d3093ff7d0>
Warning message:
In dir.create(new.directory) :
'F:\biocbuild\bbs-3.19-bioc\meat\BufferedMatrix.Rcheck\tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x000001d3093ff7d0>
> rowMedians(tmp)
[1] 0.229605395 0.103812856 0.336885321 0.498222287 -0.151075953
[6] 0.261904386 0.062212911 -0.008532495 -0.418463911 -0.558868459
[11] -0.038943666 -0.625941815 -0.216143571 -0.047448389 -0.204923510
[16] 0.299810555 0.017195504 -0.604990371 -0.018561216 -0.217400677
[21] 0.073946618 0.044356953 -0.223036722 0.144731185 -0.114598023
[26] 0.032343302 0.467985701 -0.277283319 0.264713833 -0.150511812
[31] 0.406296913 -0.048873895 -0.455418046 0.177812898 0.413247776
[36] 0.340318688 0.235307563 0.330247805 -0.099863663 -0.246118846
[41] -0.101866154 -0.340647256 0.278349542 0.058539909 -0.311249868
[46] 0.482454155 -0.590548490 -0.224387328 -0.427329739 0.031629259
[51] 0.475284795 0.296562438 -0.570564021 0.265756705 -0.029624982
[56] -0.118723252 -0.213720835 -0.161201941 0.176201485 -0.005365339
[61] -0.008853854 -0.224343611 0.087115653 -0.345569104 -0.354633746
[66] 0.315262929 0.157656190 -0.084049409 -0.313410064 -0.254687779
[71] -0.114916213 -0.031209068 -0.449236837 -1.154827287 -0.218163549
[76] -0.585537563 -0.493036462 -0.016336831 -0.085969317 -0.352392381
[81] -0.102025010 -0.072858817 -0.073196983 0.127933526 -0.003702985
[86] 0.141179223 0.038163162 0.186469682 0.790561545 0.022540665
[91] -0.197157528 0.228305590 0.086036962 0.055130202 -0.116662041
[96] 0.003113986 0.275158053 0.398996654 0.219509277 0.154689173
[101] -0.055193720 0.658043188 0.178105293 0.119680348 0.131396408
[106] -0.045112393 0.617898151 -0.120111707 0.131787249 -0.060685709
[111] -0.469508454 0.027186021 -0.333155645 -0.041290849 -0.712732163
[116] 0.041784957 -0.559294941 -0.132683898 -0.187017270 -0.517842044
[121] -0.576912100 0.038892511 -0.539992384 0.089800049 0.559857419
[126] 0.068007630 0.010543665 -0.237871053 0.237340378 -0.209112706
[131] -0.231609311 0.402835406 -0.307044336 0.482356714 0.335907905
[136] 0.409589854 -0.166995280 0.072284550 0.425590815 -0.498749768
[141] -0.208862678 0.355744820 -0.232683599 -0.076101793 0.207640907
[146] 0.502546978 0.174068874 0.117778685 0.579617348 0.034394753
[151] 0.280216154 -0.022615403 0.147974893 -0.455289764 0.198304583
[156] -0.600797059 0.041154994 0.627290120 -0.060236052 0.417816537
[161] -0.363607569 -0.120620620 -0.099196994 0.033314313 0.043224487
[166] 0.029549498 -0.246341509 -0.105175389 -0.071628221 -0.303446371
[171] 0.107020075 0.160822117 -0.150571341 -0.748226709 -0.223015510
[176] 0.529244684 0.376741130 -0.246475757 0.289842966 -0.240346425
[181] 0.425193893 -0.286648903 0.245376083 -0.134638038 0.275116393
[186] -0.077782246 0.151215453 -0.071449870 -0.005712080 -0.116033268
[191] -0.452950792 0.089252534 0.434783423 0.118528748 -0.494337297
[196] 0.035477465 0.289738555 0.005333214 -0.072114779 -0.146700763
[201] -0.403378239 -0.239149236 -0.171666681 0.388095172 0.073725177
[206] 0.349635087 -0.338715907 -0.305908614 -0.523174747 -0.408987128
[211] 0.521996699 0.379441220 -0.416758310 -0.082954761 0.065892546
[216] -0.481951564 -0.049167389 0.420329555 0.004056013 -0.019517159
[221] -0.052780381 0.092476367 0.505363582 0.404538921 -0.481628728
[226] 0.417139921 -0.011170753 0.260480881 -0.189260599 0.396023506
>
> proc.time()
user system elapsed
3.90 21.28 48.70
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000213b38fd830>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000213b38fd830>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000213b38fd830>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x00000213b38fd830>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x00000213b38fda70>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fda70>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x00000213b38fda70>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fda70>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000213b38fda70>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fd170>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fd170>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000213b38fd170>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x00000213b38fd170>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000213b38fd170>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x00000213b38fd170>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000213b38fd170>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x00000213b38fd170>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000213b38fd170>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fd1d0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x00000213b38fd1d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fd1d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fd1d0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilec6869d57deb" "BufferedMatrixFilec686ffd4aad"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilec6869d57deb" "BufferedMatrixFilec686ffd4aad"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fd6b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fd6b0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000213b38fd6b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000213b38fd6b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x00000213b38fd6b0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x00000213b38fd6b0>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fd230>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000213b38fd230>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x00000213b38fd230>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x00000213b38fd230>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000213b38fdad0>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000213b38fdad0>
> rm(P)
>
> proc.time()
user system elapsed
0.37 0.15 0.90
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.34 0.10 0.84