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CHECK report for maanova on tokay2

This page was generated on 2020-10-17 11:56:59 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE maanova PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 967/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maanova 1.58.0
Keith Sheppard
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/maanova
Branch: RELEASE_3_11
Last Commit: 13c76ca
Last Changed Date: 2020-04-27 14:12:05 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: maanova
Version: 1.58.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maanova.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings maanova_1.58.0.tar.gz
StartedAt: 2020-10-17 05:35:11 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:36:20 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 69.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: maanova.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maanova.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings maanova_1.58.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/maanova.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'maanova/DESCRIPTION' ... OK
* this is package 'maanova' version '1.58.0'
* 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 'maanova' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcPRnKX/R.INSTALL16545fbe5c4c/maanova/man/geneprofile.Rd:31: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/maanova.Rcheck/00install.out' for details.
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'qvalue' 'snow'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.consensus.hc plot.consensus.kmean print.madata
  print.summary.madata print.summary.mamodel subset.madata
  summary.madata summary.mamodel transform.madata transform.rawdata
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fdr: no visible global function definition for 'qvalue'
matest: no visible global function definition for 'makeMPIcluster'
matest: no visible global function definition for 'clusterApply'
matest: no visible global function definition for 'clusterEvalQ'
matest: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  clusterApply clusterEvalQ makeMPIcluster qvalue stopCluster
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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-3.11-bioc/R/library/maanova/libs/i386/maanova.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/maanova/libs/x64/maanova.dll':
  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. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/maanova.Rcheck/00check.log'
for details.



Installation output

maanova.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/maanova_1.58.0.tar.gz && rm -rf maanova.buildbin-libdir && mkdir maanova.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maanova.buildbin-libdir maanova_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL maanova_1.58.0.zip && rm maanova_1.58.0.tar.gz maanova_1.58.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  803k  100  803k    0     0  4947k      0 --:--:-- --:--:-- --:--:-- 5184k

install for i386

* installing *source* package 'maanova' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c makeratio.c -o makeratio.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c masvd.c -o masvd.o
masvd.c:114:2: warning: "/*" within comment [-Wcomment]
  /* work on a copy of x */
   
masvd.c:154:1: warning: "/*" within comment [-Wcomment]
 /*#ifndef IEEE_754
  
masvd.c:161:5: warning: "/*" within comment [-Wcomment]
     /* work on a copy of x */
      
masvd.c:165:2: warning: "/*" within comment [-Wcomment]
  /* ask for optimal size of work array */
   
masvd.c:189:2: warning: "/*" within comment [-Wcomment]
  /* ask for optimal size of work array */
   
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c shift.c -o shift.o
shift.c: In function 'shift':
shift.c:27:13: warning: unused variable 'k' [-Wunused-variable]
   int i, j, k;
             ^
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o maanova.dll tmp.def makeratio.o masvd.o shift.o util.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/maanova.buildbin-libdir/00LOCK-maanova/00new/maanova/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'maanova'
    finding HTML links ... done
    PairContrast                            html  
    Rmaanova.version                        html  
    abf1                                    html  
    adjPval                                 html  
    arrayview                               html  
    consensus                               html  
    dyeswapfilter                           html  
    fill.missing                            html  
    fitmaanova                              html  
    fom                                     html  
    geneprofile                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcPRnKX/R.INSTALL16545fbe5c4c/maanova/man/geneprofile.Rd:31: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    gridcheck                               html  
    kidney                                  html  
    maanova-internal                        html  
    macluster                               html  
    matest                                  html  
    read.madata                             html  
    resiplot                                html  
    riplot                                  html  
    subset.madata                           html  
    summarytable                            html  
    transform.madata                        html  
    varplot                                 html  
    volcano                                 html  
    write.madata                            html  
** 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

install for x64

* installing *source* package 'maanova' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c makeratio.c -o makeratio.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c masvd.c -o masvd.o
masvd.c:114:2: warning: "/*" within comment [-Wcomment]
  /* work on a copy of x */
   
masvd.c:154:1: warning: "/*" within comment [-Wcomment]
 /*#ifndef IEEE_754
  
masvd.c:161:5: warning: "/*" within comment [-Wcomment]
     /* work on a copy of x */
      
masvd.c:165:2: warning: "/*" within comment [-Wcomment]
  /* ask for optimal size of work array */
   
masvd.c:189:2: warning: "/*" within comment [-Wcomment]
  /* ask for optimal size of work array */
   
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c shift.c -o shift.o
shift.c: In function 'shift':
shift.c:27:13: warning: unused variable 'k' [-Wunused-variable]
   int i, j, k;
             ^
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o maanova.dll tmp.def makeratio.o masvd.o shift.o util.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/maanova.buildbin-libdir/maanova/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maanova' as maanova_1.58.0.zip
* DONE (maanova)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'maanova' successfully unpacked and MD5 sums checked

Tests output


Example timings

maanova.Rcheck/examples_i386/maanova-Ex.timings

nameusersystemelapsed
PairContrast0.010.010.03
Rmaanova.version0.020.000.01
abf10.020.000.01
adjPval0.000.020.02
arrayview000
consensus0.020.000.01
dyeswapfilter000
fill.missing0.220.050.27
fitmaanova0.010.000.01
fom0.000.010.02
geneprofile0.000.020.01
gridcheck000
kidney0.090.000.09
maanova-internal000
macluster0.010.000.01
matest0.000.010.02
read.madata0.020.000.02
resiplot0.020.000.01
riplot000
subset.madata0.090.000.10
summarytable0.010.000.01
transform.madata0.070.020.08
varplot000
volcano000
write.madata000

maanova.Rcheck/examples_x64/maanova-Ex.timings

nameusersystemelapsed
PairContrast0.030.000.03
Rmaanova.version0.010.000.02
abf10.010.000.02
adjPval0.000.020.01
arrayview000
consensus0.020.000.02
dyeswapfilter000
fill.missing0.120.010.14
fitmaanova0.020.000.01
fom0.020.000.02
geneprofile0.010.000.02
gridcheck000
kidney0.100.000.09
maanova-internal000
macluster0.000.020.01
matest0.010.000.02
read.madata000
resiplot0.000.020.02
riplot000
subset.madata0.080.010.09
summarytable0.000.020.02
transform.madata0.080.010.09
varplot000
volcano000
write.madata0.000.020.02