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CHECK report for genoCN on malbec2

This page was generated on 2018-10-17 08:23:01 -0400 (Wed, 17 Oct 2018).

Package 585/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoCN 1.32.0
Wei Sun
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/genoCN
Branch: RELEASE_3_7
Last Commit: a2de30a
Last Changed Date: 2018-04-30 10:35:13 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genoCN
Version: 1.32.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:genoCN.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings genoCN_1.32.0.tar.gz
StartedAt: 2018-10-16 00:41:54 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:42:38 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 43.6 seconds
RetCode: 0
Status:  OK 
CheckDir: genoCN.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:genoCN.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings genoCN_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/genoCN.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoCN’ version ‘1.32.0’
* 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 ‘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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
genoCNA 21.996   0.02  22.029
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/genoCN.Rcheck/00check.log’
for details.



Installation output

genoCN.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL genoCN
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘genoCN’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c tnorm_mle.c -o tnorm_mle.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utility.c -o utility.o
utility.c: In function ‘readfile’:
utility.c:155:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
             fscanf(file,"%s",temp);
             ^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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: ‘nGtp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
                 ^
xCNV.c:1839:17: warning: ‘pbf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o genoCN.so tnorm_mle.o utility.o xCNV.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/genoCN/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genoCN)

Tests output


Example timings

genoCN.Rcheck/genoCN-Ex.timings

nameusersystemelapsed
genoCNA21.996 0.02022.029
genoCNV1.6720.0081.683
init.Para.CNA0.0040.0000.001
init.Para.CNV0.0000.0000.001
plotCN0.1760.0040.180
snpData0.1760.0040.181
snpInfo0.1720.0120.184