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BioC 3.6: CHECK report for geneXtendeR on tokay1

This page was generated on 2017-08-16 13:37:00 -0400 (Wed, 16 Aug 2017).

Package 536/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneXtendeR 1.3.5
Bohdan Khomtchouk
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/geneXtendeR
Last Changed Rev: 131878 / Revision: 131943
Last Changed Date: 2017-08-09 20:38:47 -0400 (Wed, 09 Aug 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneXtendeR
Version: 1.3.5
Command: rm -rf geneXtendeR.buildbin-libdir geneXtendeR.Rcheck && mkdir geneXtendeR.buildbin-libdir geneXtendeR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=geneXtendeR.buildbin-libdir geneXtendeR_1.3.5.tar.gz >geneXtendeR.Rcheck\00install.out 2>&1 && cp geneXtendeR.Rcheck\00install.out geneXtendeR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=geneXtendeR.buildbin-libdir --install="check:geneXtendeR-install.out" --force-multiarch --no-vignettes --timings geneXtendeR_1.3.5.tar.gz
StartedAt: 2017-08-15 23:44:15 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-16 00:03:57 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 1182.0 seconds
RetCode: 0
Status:  OK  
CheckDir: geneXtendeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf geneXtendeR.buildbin-libdir geneXtendeR.Rcheck && mkdir geneXtendeR.buildbin-libdir geneXtendeR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=geneXtendeR.buildbin-libdir geneXtendeR_1.3.5.tar.gz >geneXtendeR.Rcheck\00install.out 2>&1 && cp geneXtendeR.Rcheck\00install.out geneXtendeR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=geneXtendeR.buildbin-libdir --install="check:geneXtendeR-install.out" --force-multiarch --no-vignettes --timings geneXtendeR_1.3.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/geneXtendeR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneXtendeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geneXtendeR' version '1.3.5'
* 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 'geneXtendeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data      5.8Mb
    extdata   1.2Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'RColorBrewer' 'SnowballC' 'networkD3' 'org.Ag.eg.db' 'org.Bt.eg.db'
  'org.Ce.eg.db' 'org.Cf.eg.db' 'org.Dm.eg.db' 'org.Dr.eg.db'
  'org.Gg.eg.db' 'org.Hs.eg.db' 'org.Mm.eg.db' 'org.Mmu.eg.db'
  'org.Pt.eg.db' 'org.Sc.sgd.db' 'org.Ss.eg.db' 'org.Xl.eg.db'
  'wordcloud'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'GO.db' 'org.Rn.eg.db'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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'
cumlinePlot : geneXtender: no visible binding for global variable
  'type'
cumlinePlot : geneXtender: no visible binding for global variable
  'seqid'
cumlinePlot : geneXtender: no visible binding for global variable
  'gene_id'
cumlinePlot : geneXtender: no visible binding for global variable
  'gene_name'
diffGO : geneXtender: no visible binding for global variable 'type'
diffGO : geneXtender: no visible binding for global variable 'seqid'
diffGO : geneXtender: no visible binding for global variable 'gene_id'
diffGO : geneXtender: no visible binding for global variable
  'gene_name'
diffGO: no visible binding for global variable 'GO.db'
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'
hotspotPlot : geneXtender: no visible binding for global variable
  'type'
hotspotPlot : geneXtender: no visible binding for global variable
  'seqid'
hotspotPlot : geneXtender: no visible binding for global variable
  'gene_id'
hotspotPlot : 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'
makeNetwork : geneXtender: no visible binding for global variable
  'type'
makeNetwork : geneXtender: no visible binding for global variable
  'seqid'
makeNetwork : geneXtender: no visible binding for global variable
  'gene_id'
makeNetwork : geneXtender: no visible binding for global variable
  'gene_name'
makeNetwork: no visible binding for global variable 'GO.db'
makeNetwork: no visible global function definition for '%>%'
makeNetwork: no visible global function definition for 'left_join'
makeNetwork: no visible global function definition for 'rename'
makeNetwork: no visible binding for global variable 'id'
makeNetwork: no visible global function definition for 'forceNetwork'
makeNetwork: no visible global function definition for 'JS'
makeWordCloud : geneXtender: no visible binding for global variable
  'type'
makeWordCloud : geneXtender: no visible binding for global variable
  'seqid'
makeWordCloud : geneXtender: no visible binding for global variable
  'gene_id'
makeWordCloud : geneXtender: no visible binding for global variable
  'gene_name'
makeWordCloud: no visible binding for global variable 'GO.db'
makeWordCloud: no visible global function definition for 'VectorSource'
makeWordCloud: no visible binding for global variable 'removeWords'
makeWordCloud: no visible global function definition for 'stopwords'
makeWordCloud: no visible global function definition for 'wordcloud'
makeWordCloud: no visible global function definition for 'brewer.pal'
meanPeakLength : geneXtender: no visible binding for global variable
  'type'
meanPeakLength : geneXtender: no visible binding for global variable
  'seqid'
meanPeakLength : geneXtender: no visible binding for global variable
  'gene_id'
meanPeakLength : geneXtender: no visible binding for global variable
  'gene_name'
peaksInput: no visible binding for global variable 'chr'
peaksMerge: no visible binding for global variable 'chr'
peaksMerge: no visible binding for global variable 'g'
peaksMerge: no visible global function definition for '.'
plotWordFreq : geneXtender: no visible binding for global variable
  'type'
plotWordFreq : geneXtender: no visible binding for global variable
  'seqid'
plotWordFreq : geneXtender: no visible binding for global variable
  'gene_id'
plotWordFreq : geneXtender: no visible binding for global variable
  'gene_name'
plotWordFreq: no visible binding for global variable 'GO.db'
plotWordFreq: no visible global function definition for 'VectorSource'
plotWordFreq: no visible binding for global variable 'removeWords'
plotWordFreq: no visible global function definition for 'stopwords'
Undefined global functions or variables:
  %>% . GO.db JS VectorSource brewer.pal chr forceNetwork g gene_id
  gene_name id left_join removeWords rename seqid stopwords type
  wordcloud
* 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-3.6-bioc/meat/geneXtendeR.buildbin-libdir/geneXtendeR/libs/i386/geneXtendeR.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 the system RNG.
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 or elapsed time > 5s
                    user system elapsed
meanPeakLengthPlot 55.86   0.89   58.79
hotspotPlot        42.01   0.67   48.33
linePlot           32.64   0.59   35.16
barChart           30.11   0.61   38.04
cumlinePlot        29.99   0.37   32.61
makeNetwork        21.81   0.52   25.85
plotWordFreq       21.42   0.45   24.00
makeWordCloud      21.05   0.48   25.20
annotate           20.99   0.50   25.09
diffGO             20.61   0.49   31.26
distinct           19.86   0.39   22.31
peakLengthBoxplot  18.58   0.27   20.88
meanPeakLength     17.92   0.31   21.36
rat                 4.95   0.30    5.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
meanPeakLengthPlot 60.56   0.68   63.53
hotspotPlot        41.33   0.48   51.27
cumlinePlot        36.98   0.41   39.67
barChart           30.05   0.61   32.58
linePlot           27.15   0.47   31.54
makeWordCloud      24.77   0.38   27.41
meanPeakLength     23.92   0.19   26.36
annotate           23.02   0.48   26.89
makeNetwork        20.97   0.34   23.36
distinct           21.05   0.22   24.62
diffGO             20.41   0.34   23.10
plotWordFreq       18.56   0.25   24.91
peakLengthBoxplot  18.38   0.33   30.22
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/geneXtendeR.Rcheck/00check.log'
for details.


geneXtendeR.Rcheck/00install.out:


install for i386

* installing *source* package 'geneXtendeR' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c annotate.c -o annotate.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c extract_peaks.c -o extract_peaks.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/geneXtendeR.buildbin-libdir/geneXtendeR/libs/i386
** 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

install for x64

* installing *source* package 'geneXtendeR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c annotate.c -o annotate.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c extract_peaks.c -o extract_peaks.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/geneXtendeR.buildbin-libdir/geneXtendeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneXtendeR' as geneXtendeR_1.3.5.zip
* DONE (geneXtendeR)

geneXtendeR.Rcheck/examples_i386/geneXtendeR-Ex.timings:

nameusersystemelapsed
allPeakLengths0.030.020.05
annotate20.99 0.5025.09
barChart30.11 0.6138.04
cumlinePlot29.99 0.3732.61
diffGO20.61 0.4931.26
distinct19.86 0.3922.31
hotspotPlot42.01 0.6748.33
linePlot32.64 0.5935.16
makeNetwork21.81 0.5225.85
makeWordCloud21.05 0.4825.20
meanPeakLength17.92 0.3121.36
meanPeakLengthPlot55.86 0.8958.79
peakLengthBoxplot18.58 0.2720.88
peaksInput0.330.020.97
peaksMerge0.130.030.15
plotWordFreq21.42 0.4524.00
rat4.950.305.25
samplepeaksinput000

geneXtendeR.Rcheck/examples_x64/geneXtendeR-Ex.timings:

nameusersystemelapsed
allPeakLengths0.030.000.03
annotate23.02 0.4826.89
barChart30.05 0.6132.58
cumlinePlot36.98 0.4139.67
diffGO20.41 0.3423.10
distinct21.05 0.2224.62
hotspotPlot41.33 0.4851.27
linePlot27.15 0.4731.54
makeNetwork20.97 0.3423.36
makeWordCloud24.77 0.3827.41
meanPeakLength23.92 0.1926.36
meanPeakLengthPlot60.56 0.6863.53
peakLengthBoxplot18.38 0.3330.22
peaksInput0.170.070.23
peaksMerge0.150.000.18
plotWordFreq18.56 0.2524.91
rat4.060.184.25
samplepeaksinput0.020.000.01