Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:29 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 247/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BufferedMatrixMethods 1.66.0  (landing page)
Ben Bolstad
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/BufferedMatrixMethods
git_branch: RELEASE_3_18
git_last_commit: be08e2e
git_last_commit_date: 2023-10-24 09:37:53 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for BufferedMatrixMethods on kunpeng2


To the developers/maintainers of the BufferedMatrixMethods package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrixMethods.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: BufferedMatrixMethods
Version: 1.66.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BufferedMatrixMethods.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BufferedMatrixMethods_1.66.0.tar.gz
StartedAt: 2023-11-02 08:55:21 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 08:55:42 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 20.9 seconds
RetCode: 0
Status:   OK  
CheckDir: BufferedMatrixMethods.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BufferedMatrixMethods.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BufferedMatrixMethods_1.66.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BufferedMatrixMethods.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrixMethods/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BufferedMatrixMethods’ version ‘1.66.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrixMethods’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘affy’ ‘affyio’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘BufferedMatrix’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
  .Call("read_probeintensities", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

BufferedMatrix.bg.correct.normalize.quantiles: no visible global
  function definition for ‘is’
BufferedMatrix.bg.correct.normalize.quantiles: no visible global
  function definition for ‘duplicate’
BufferedMatrix.bg.correct.normalize.quantiles : bg.dens: no visible
  global function definition for ‘density’
BufferedMatrix.justRMA: no visible global function definition for ‘new’
BufferedMatrix.justRMA: no visible global function definition for
  ‘pData’
BufferedMatrix.justRMA: no visible global function definition for
  ‘read.celfile.header’
BufferedMatrix.justRMA: no visible global function definition for
  ‘cleancdfname’
BufferedMatrix.justRMA: no visible global function definition for
  ‘pmindex’
BufferedMatrix.justRMA: no visible global function definition for
  ‘geneNames’
BufferedMatrix.justRMA: no visible global function definition for
  ‘set.buffer.dim’
BufferedMatrix.justRMA: no visible global function definition for
  ‘RowMode’
BufferedMatrix.justRMA: no visible global function definition for
  ‘notes<-’
BufferedMatrix.read.celfiles: no visible global function definition for
  ‘createBufferedMatrix’
BufferedMatrix.read.celfiles: no visible global function definition for
  ‘read.celfile’
BufferedMatrix.read.celfiles: no visible global function definition for
  ‘AddColumn’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘new’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘cleancdfname’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘getCdfInfo’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘createBufferedMatrix’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘AddColumn’
bg.correct.BufferedMatrix: no visible global function definition for
  ‘is’
bg.correct.BufferedMatrix: no visible global function definition for
  ‘duplicate’
bg.correct.BufferedMatrix : bg.dens: no visible global function
  definition for ‘density’
normalize.BufferedMatrix.quantiles: no visible global function
  definition for ‘is’
normalize.BufferedMatrix.quantiles: no visible global function
  definition for ‘duplicate’
Undefined global functions or variables:
  AddColumn RowMode cleancdfname createBufferedMatrix density duplicate
  geneNames getCdfInfo is new notes<- pData pmindex read.celfile
  read.celfile.header set.buffer.dim
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "density")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 is not available
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BufferedMatrixMethods.Rcheck/00check.log’
for details.



Installation output

BufferedMatrixMethods.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL BufferedMatrixMethods
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘BufferedMatrixMethods’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/BufferedMatrix/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c init_package.c -o init_package.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/BufferedMatrix/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c preprocess_bm.c -o preprocess_bm.o
preprocess_bm.c: In function ‘bm_rma_bg_correct’:
preprocess_bm.c:344:7: warning: unused variable ‘i’ [-Wunused-variable]
  344 |   int i,j;
      |       ^
preprocess_bm.c: In function ‘R_bm_rma_bg_correct’:
preprocess_bm.c:378:7: warning: unused variable ‘current_mode’ [-Wunused-variable]
  378 |   int current_mode;
      |       ^~~~~~~~~~~~
preprocess_bm.c: In function ‘R_bm_quantile_normalize’:
preprocess_bm.c:593:7: warning: unused variable ‘current_mode’ [-Wunused-variable]
  593 |   int current_mode;
      |       ^~~~~~~~~~~~
preprocess_bm.c: In function ‘do_RMA_buffmat’:
preprocess_bm.c:924:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
  924 |   int first_ind;
      |       ^~~~~~~~~
preprocess_bm.c: In function ‘R_bm_rma_bg_correct_quantile_normalize’:
preprocess_bm.c:1151:7: warning: unused variable ‘current_mode’ [-Wunused-variable]
 1151 |   int current_mode;
      |       ^~~~~~~~~~~~
At top level:
preprocess_bm.c:453:12: warning: ‘min’ defined but not used [-Wunused-function]
  453 | static int min(int x1,int x2){
      |            ^~~
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o BufferedMatrixMethods.so init_package.o preprocess_bm.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-BufferedMatrixMethods/00new/BufferedMatrixMethods/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrixMethods)

Tests output


Example timings