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CHECK report for ADaCGH2 on tokay1

This page was generated on 2020-07-30 11:54:57 -0400 (Thu, 30 Jul 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ADaCGH2 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 15/1879HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ADaCGH2 2.29.0
Ramon Diaz-Uriarte
Snapshot Date: 2020-07-29 14:50:08 -0400 (Wed, 29 Jul 2020)
URL: https://git.bioconductor.org/packages/ADaCGH2
Branch: master
Last Commit: 31c21bb
Last Changed Date: 2020-04-27 14:23:32 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ADaCGH2
Version: 2.29.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ADaCGH2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ADaCGH2_2.29.0.tar.gz
StartedAt: 2020-07-30 00:28:44 -0400 (Thu, 30 Jul 2020)
EndedAt: 2020-07-30 00:33:59 -0400 (Thu, 30 Jul 2020)
EllapsedTime: 315.5 seconds
RetCode: 0
Status:  OK  
CheckDir: ADaCGH2.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ADaCGH2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ADaCGH2_2.29.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ADaCGH2.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ADaCGH2/DESCRIPTION' ... OK
* this is package 'ADaCGH2' version '2.29.0'
* 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 'ADaCGH2' 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
* 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-3.12-bioc/R/library/ADaCGH2/libs/i386/ADaCGH2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/ADaCGH2/libs/x64/ADaCGH2.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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
pChromPlot         23.19   0.09   23.69
pSegment           16.55   0.02   16.56
outputToCGHregions 11.51   0.09   11.63
inputToADaCGH       6.08   0.05    6.93
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
pChromPlot         24.19   0.03   24.47
pSegment           19.72   0.00   19.73
outputToCGHregions 11.02   0.04   11.07
inputToADaCGH       5.47   0.04    6.13
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ADaCGH2.Rcheck/00check.log'
for details.



Installation output

ADaCGH2.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ADaCGH2_2.29.0.tar.gz && rm -rf ADaCGH2.buildbin-libdir && mkdir ADaCGH2.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ADaCGH2.buildbin-libdir ADaCGH2_2.29.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ADaCGH2_2.29.0.zip && rm ADaCGH2_2.29.0.tar.gz ADaCGH2_2.29.0.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  720k  100  720k    0     0  14.7M      0 --:--:-- --:--:-- --:--:-- 15.9M

install for i386

* installing *source* package 'ADaCGH2' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable]
     double totalNorm;
            ^~~~~~~~~
r_haarseg.c: In function 'ad_FindLocalPeaks':
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
       }/* for j */
         
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
       }/* for j */
         
r_haarseg.c:128:9: warning: unused variable 'j' [-Wunused-variable]
   int k,j;
         ^
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:97:27: warning: 'highNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
             highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1];
             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:96:26: warning: 'lowNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
             lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1];
             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:99:27: warning: 'highWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
             highWeightSum += weight[highEnd] - weight[k-1];
             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:98:26: warning: 'lowWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
             lowWeightSum += weight[k-1] - weight[lowEnd];
             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ADaCGH2.buildbin-libdir/00LOCK-ADaCGH2/00new/ADaCGH2/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ADaCGH2'
    finding HTML links ... done
    cutFile                                 html  
    inputEx                                 html  
    inputToADaCGH                           html  
    finding level-2 HTML links ... done

    outputToCGHregions                      html  
    pChromPlot                              html  
    pSegment                                html  
** building package indices
** installing vignettes
   'ADaCGH2.Rnw' using 'latin1' 
** 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 'ADaCGH2' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable]
     double totalNorm;
            ^~~~~~~~~
r_haarseg.c: In function 'ad_FindLocalPeaks':
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
       }/* for j */
         
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
       }/* for j */
         
r_haarseg.c:128:9: warning: unused variable 'j' [-Wunused-variable]
   int k,j;
         ^
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:97:27: warning: 'highNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
             highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1];
             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:96:26: warning: 'lowNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
             lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1];
             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:99:27: warning: 'highWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
             highWeightSum += weight[highEnd] - weight[k-1];
             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:98:26: warning: 'lowWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
             lowWeightSum += weight[k-1] - weight[lowEnd];
             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ADaCGH2.buildbin-libdir/ADaCGH2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ADaCGH2' as ADaCGH2_2.29.0.zip
* DONE (ADaCGH2)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ADaCGH2' successfully unpacked and MD5 sums checked

Tests output


Example timings

ADaCGH2.Rcheck/examples_i386/ADaCGH2-Ex.timings

nameusersystemelapsed
cutFile000
inputToADaCGH6.080.056.93
outputToCGHregions11.51 0.0911.63
pChromPlot23.19 0.0923.69
pSegment16.55 0.0216.56

ADaCGH2.Rcheck/examples_x64/ADaCGH2-Ex.timings

nameusersystemelapsed
cutFile000
inputToADaCGH5.470.046.13
outputToCGHregions11.02 0.0411.07
pChromPlot24.19 0.0324.47
pSegment19.72 0.0019.73