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CHECK report for discordant on tokay2

This page was generated on 2020-10-17 11:56:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE discordant PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 480/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
discordant 1.12.0
Charlotte Siska
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/discordant
Branch: RELEASE_3_11
Last Commit: 29818da
Last Changed Date: 2020-04-27 15:04:58 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS 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  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: discordant
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:discordant.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings discordant_1.12.0.tar.gz
StartedAt: 2020-10-17 03:25:52 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:26:58 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 65.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: discordant.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:discordant.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings discordant_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/discordant.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 'discordant/DESCRIPTION' ... OK
* this is package 'discordant' version '1.12.0'
* package encoding: latin1
* 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 'discordant' can be installed ... WARNING
Found the following significant warnings:
  discordant.c:21:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  discordant.c:147:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/discordant.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 ... 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 ... 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 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/discordant/libs/i386/discordant.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/discordant/libs/x64/discordant.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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/discordant.Rcheck/00check.log'
for details.



Installation output

discordant.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/discordant_1.12.0.tar.gz && rm -rf discordant.buildbin-libdir && mkdir discordant.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=discordant.buildbin-libdir discordant_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL discordant_1.12.0.zip && rm discordant_1.12.0.tar.gz discordant_1.12.0.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  189k  100  189k    0     0  2840k      0 --:--:-- --:--:-- --:--:-- 3156k

install for i386

* installing *source* package 'discordant' ...
** 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 discordant.c -o discordant.o
discordant.c: In function 'em_normal_partial_concordant':
discordant.c:21:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   while(flag>0 & iter<(*iteration)){
         ~~~~^~
discordant.c:147:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   while(flag>0 & iter<(*iteration)){
         ~~~~^~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o discordant.dll tmp.def discordant.o -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/discordant.buildbin-libdir/00LOCK-discordant/00new/discordant/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'discordant'
    finding HTML links ... done
    TCGA_Breast_RNASeq                      html  
    TCGA_Breast_RNASeq_voom                 html  
    TCGA_Breast_miRNASeq                    html  
    TCGA_Breast_miRNASeq_voom               html  
    TCGA_GBM_miRNA_microarray               html  
    TCGA_GBM_transcript_microarray          html  
    createVectors                           html  
    discordantRun                           html  
    fishersTrans                            html  
    split.MADOutlier                        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 'discordant' ...
** 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 discordant.c -o discordant.o
discordant.c: In function 'em_normal_partial_concordant':
discordant.c:21:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   while(flag>0 & iter<(*iteration)){
         ~~~~^~
discordant.c:147:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   while(flag>0 & iter<(*iteration)){
         ~~~~^~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o discordant.dll tmp.def discordant.o -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/discordant.buildbin-libdir/discordant/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'discordant' as discordant_1.12.0.zip
* DONE (discordant)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'discordant' successfully unpacked and MD5 sums checked

Tests output


Example timings

discordant.Rcheck/examples_i386/discordant-Ex.timings

nameusersystemelapsed
createVectors0.030.000.03
discordantRun1.600.001.59
fishersTrans000
split.MADOutlier0.030.020.05

discordant.Rcheck/examples_x64/discordant-Ex.timings

nameusersystemelapsed
createVectors0.030.000.03
discordantRun1.720.011.73
fishersTrans0.020.020.03
split.MADOutlier0.080.000.08