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CHECK report for genoCN on tokay1

This page was generated on 2019-04-13 11:21:11 -0400 (Sat, 13 Apr 2019).

Package 616/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoCN 1.34.0
Wei Sun
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/genoCN
Branch: RELEASE_3_8
Last Commit: 98a342d
Last Changed Date: 2018-10-30 11:41:46 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genoCN
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genoCN.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings genoCN_1.34.0.tar.gz
StartedAt: 2019-04-13 02:31:32 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:33:51 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 138.5 seconds
RetCode: 0
Status:  OK  
CheckDir: genoCN.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genoCN.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings genoCN_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/genoCN.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genoCN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoCN' version '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'genoCN' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* 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 ... NOTE
genoCNA: no visible binding for global variable 'init.Para.CNA'
genoCNV: no visible binding for global variable 'init.Para.CNV'
Undefined global functions or variables:
  init.Para.CNA init.Para.CNV
* 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-3.8-bioc/R/library/genoCN/libs/i386/genoCN.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
Examples with CPU or elapsed time > 5s
        user system elapsed
genoCNA 26.5   0.46   26.98
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
genoCNA 12.78   0.59   13.37
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/genoCN.Rcheck/00check.log'
for details.



Installation output

genoCN.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/genoCN_1.34.0.tar.gz && rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoCN.buildbin-libdir genoCN_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL genoCN_1.34.0.zip && rm genoCN_1.34.0.tar.gz genoCN_1.34.0.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  740k  100  740k    0     0  13.0M      0 --:--:-- --:--:-- --:--:-- 13.9M

install for i386

* installing *source* package 'genoCN' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c tnorm_mle.c -o tnorm_mle.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utility.c -o utility.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                         ^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                ^
xCNV.c: In function 'baum_welch':
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
   double mu_b_tmp, sd_b_tmp;
                    ^
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
   double mu_b_tmp, sd_b_tmp;
          ^
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
   int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
          ^
xCNV.c:1839:17: warning: 'pbf' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
                 ^
xCNV.c:1839:17: warning: 'nGtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/genoCN.buildbin-libdir/genoCN/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'genoCN'
    finding HTML links ... done
    code.genotype                           html  
    genoCNA                                 html  
    genoCNV                                 html  
    init.Para.CNA                           html  
    init.Para.CNV                           html  
    plotCN                                  html  
    snpData                                 html  
    snpInfo                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'genoCN' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c tnorm_mle.c -o tnorm_mle.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utility.c -o utility.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                         ^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                ^
xCNV.c: In function 'baum_welch':
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
   double mu_b_tmp, sd_b_tmp;
                    ^
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
   double mu_b_tmp, sd_b_tmp;
          ^
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
   int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
          ^
xCNV.c:1839:17: warning: 'pbf' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
                 ^
xCNV.c:1839:17: warning: 'nGtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/genoCN.buildbin-libdir/genoCN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genoCN' as genoCN_1.34.0.zip
* DONE (genoCN)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'genoCN' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

genoCN.Rcheck/examples_i386/genoCN-Ex.timings

nameusersystemelapsed
genoCNA26.50 0.4626.98
genoCNV4.280.104.38
init.Para.CNA000
init.Para.CNV000
plotCN0.260.000.27
snpData0.270.030.29
snpInfo0.260.000.27

genoCN.Rcheck/examples_x64/genoCN-Ex.timings

nameusersystemelapsed
genoCNA12.78 0.5913.37
genoCNV2.390.072.45
init.Para.CNA0.000.010.02
init.Para.CNV000
plotCN0.230.000.23
snpData0.250.000.25
snpInfo0.240.000.24