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CHECK report for genoCN on malbec2

This page was generated on 2019-10-16 11:58:14 -0400 (Wed, 16 Oct 2019).

Package 647/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoCN 1.36.0
Wei Sun
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/genoCN
Branch: RELEASE_3_9
Last Commit: 0bf64cd
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genoCN
Version: 1.36.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:genoCN.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings genoCN_1.36.0.tar.gz
StartedAt: 2019-10-16 01:53:06 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:53:43 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 36.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: genoCN.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:genoCN.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings genoCN_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/genoCN.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.36.0’
* 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 ... WARNING
Found the following significant warnings:
  utility.c:155:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/genoCN.Rcheck/00install.out’ for details.
* 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 7.984   0.04   8.025
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/genoCN.Rcheck/00check.log’
for details.



Installation output

genoCN.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL genoCN
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘genoCN’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o genoCN.so tnorm_mle.o utility.o xCNV.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-genoCN/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genoCN)

Tests output


Example timings

genoCN.Rcheck/genoCN-Ex.timings

nameusersystemelapsed
genoCNA7.9840.0408.025
genoCNV1.6560.0081.664
init.Para.CNA0.0010.0000.001
init.Para.CNV0.0010.0000.000
plotCN0.1750.0040.179
snpData0.1870.0040.191
snpInfo0.2850.0040.289