AneuFinder 1.2.1
Aaron Taudt
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/AneuFinder | | Last Changed Rev: 125058 / Revision: 128728 | | Last Changed Date: 2016-12-13 02:52:38 -0500 (Tue, 13 Dec 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ ERROR ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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###
### Running command:
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### rm -rf AneuFinder.buildbin-libdir AneuFinder.Rcheck && mkdir AneuFinder.buildbin-libdir AneuFinder.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AneuFinder.buildbin-libdir AneuFinder_1.2.1.tar.gz >AneuFinder.Rcheck\00install.out 2>&1 && cp AneuFinder.Rcheck\00install.out AneuFinder-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=AneuFinder.buildbin-libdir --install="check:AneuFinder-install.out" --force-multiarch --no-vignettes --timings AneuFinder_1.2.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/AneuFinder.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AneuFinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AneuFinder' version '1.2.1'
* 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 'AneuFinder' can be installed ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 ... NOTE
Aneufinder: multiple local function definitions for 'parallel.helper'
with different formal arguments
* checking Rd files ... OK
* 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.4-bioc/meat/AneuFinder.buildbin-libdir/AneuFinder/libs/i386/AneuFinder.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
simulateReads 97.03 3.36 100.77
correctGC 73.05 2.89 84.64
getSCEcoordinates 34.14 0.22 35.80
heatmapAneuploidies 25.03 0.13 25.18
findCNVs.strandseq 23.26 0.21 24.81
heatmapGenomewide 17.80 0.06 17.97
findCNVs 10.18 0.39 11.55
binReads 7.36 0.28 8.92
collapseBins 6.58 0.31 7.98
variableWidthBins 5.95 0.40 19.25
bed2GRanges 5.55 0.28 7.11
** running examples for arch 'x64' ... ERROR
Running examples in 'AneuFinder-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: correctGC
> ### Title: GC correction
> ### Aliases: correctGC
>
> ### ** Examples
>
> ## Get a BED file, bin it and run GC correction
> bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData")
> binned <- binReads(bedfile, assembly='mm10', binsize=1e6,
+ chromosomes=c(1:19,'X','Y'))
Reading file KK150311_VI_07.bam.bed.gz ... 1.99s
Fetching chromosome lengths from UCSC ...Error in function (type, msg, asError = TRUE) :
Operation timed out after 0 milliseconds with 0 out of 0 bytes received
Calls: binReads ... getURL -> curlPerform -> .Call -> <Anonymous> -> fun
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/AneuFinder.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'AneuFinder' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c R_interface.cpp -o R_interface.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c densities.cpp -o densities.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c loghmm.cpp -o loghmm.o
loghmm.cpp:320:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
loghmm.cpp:480:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
loghmm.cpp:518:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
loghmm.cpp:583:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:400:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:694:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:732:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:791:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c utility.cpp -o utility.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/AneuFinder.buildbin-libdir/AneuFinder/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'AneuFinder' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c R_interface.cpp -o R_interface.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c densities.cpp -o densities.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c loghmm.cpp -o loghmm.o
loghmm.cpp:320:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
loghmm.cpp:480:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
loghmm.cpp:518:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
loghmm.cpp:583:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:400:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:694:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:732:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:791:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c utility.cpp -o utility.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/AneuFinder.buildbin-libdir/AneuFinder/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AneuFinder' as AneuFinder_1.2.1.zip
* DONE (AneuFinder)