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BioC 3.5: CHECK report for geneXtendeR on malbec2

This page was generated on 2017-10-18 14:18:07 -0400 (Wed, 18 Oct 2017).

Package 529/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneXtendeR 1.2.0
Bohdan Khomtchouk
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/geneXtendeR
Branch: RELEASE_3_5
Last Commit: 66031a3
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneXtendeR
Version: 1.2.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings geneXtendeR_1.2.0.tar.gz
StartedAt: 2017-10-17 23:28:26 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:33:21 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 294.9 seconds
RetCode: 0
Status:  OK 
CheckDir: geneXtendeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings geneXtendeR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/geneXtendeR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneXtendeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneXtendeR’ version ‘1.2.0’
* 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 ‘geneXtendeR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
* 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
* 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 loading without being on the library search path ... 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
annotate : geneXtender: no visible binding for global variable ‘type’
annotate : geneXtender: no visible binding for global variable ‘seqid’
annotate : geneXtender: no visible binding for global variable
  ‘gene_id’
annotate : geneXtender: no visible binding for global variable
  ‘gene_name’
barChart : geneXtender: no visible binding for global variable ‘type’
barChart : geneXtender: no visible binding for global variable ‘seqid’
barChart : geneXtender: no visible binding for global variable
  ‘gene_id’
barChart : geneXtender: no visible binding for global variable
  ‘gene_name’
distinct : geneXtender: no visible binding for global variable ‘type’
distinct : geneXtender: no visible binding for global variable ‘seqid’
distinct : geneXtender: no visible binding for global variable
  ‘gene_id’
distinct : geneXtender: no visible binding for global variable
  ‘gene_name’
linePlot : geneXtender: no visible binding for global variable ‘type’
linePlot : geneXtender: no visible binding for global variable ‘seqid’
linePlot : geneXtender: no visible binding for global variable
  ‘gene_id’
linePlot : geneXtender: no visible binding for global variable
  ‘gene_name’
peaksInput: no visible binding for global variable ‘chr’
Undefined global functions or variables:
  chr gene_id gene_name seqid type
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
barChart 22.296  0.280  25.219
linePlot 20.116  0.392  23.012
annotate 16.268  0.600  19.626
distinct 11.848  0.284  15.017
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.


geneXtendeR.Rcheck/00install.out:

* installing *source* package ‘geneXtendeR’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c annotate.c -o annotate.o
annotate.c: In function ‘annotate’:
annotate.c:102:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(varstr, 50000, varfp);
     ^
annotate.c:112:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(vcfstr, 10000, vcffp);
     ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c extract_number.c -o extract_number.o
extract_number.c: In function ‘extractnumber’:
extract_number.c:72:10: warning: variable ‘n_1’ set but not used [-Wunused-but-set-variable]
     long n_1;
          ^
extract_number.c:66:10: warning: variable ‘j_1’ set but not used [-Wunused-but-set-variable]
     long j_1;
          ^
extract_number.c:54:12: warning: variable ‘pvcfcol5_5’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol5_5;
            ^
extract_number.c:53:12: warning: variable ‘pvcfcol4_4’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol4_4;
            ^
extract_number.c:52:12: warning: variable ‘pvcfcol3_3’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol3_3;
            ^
extract_number.c:51:12: warning: variable ‘pvcfcol2_2’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol2_2;
            ^
extract_number.c:50:12: warning: variable ‘pvcfcol1_1’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol1_1;
            ^
extract_number.c:98:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(varstr, 50000, varfp);
     ^
extract_number.c:108:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(vcfstr, 10000, vcffp);
     ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c extract_peaks.c -o extract_peaks.o
extract_peaks.c: In function ‘extractpeaks’:
extract_peaks.c:103:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(varstr, 50000, varfp);
     ^
extract_peaks.c:113:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(vcfstr, 10000, vcffp);
     ^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/geneXtendeR.Rcheck/geneXtendeR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geneXtendeR)

geneXtendeR.Rcheck/geneXtendeR-Ex.timings:

nameusersystemelapsed
annotate16.268 0.60019.626
barChart22.296 0.28025.219
distinct11.848 0.28415.017
linePlot20.116 0.39223.012
peaksInput0.2320.0440.826
rat3.8641.0164.885
samplepeaksinput0.0080.0000.009