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CHECK report for geneXtendeR on tokay2

This page was generated on 2018-10-17 08:42:59 -0400 (Wed, 17 Oct 2018).

Package 583/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneXtendeR 1.6.0
Bohdan Khomtchouk
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/geneXtendeR
Branch: RELEASE_3_7
Last Commit: d0e86e9
Last Changed Date: 2018-04-30 10:35:44 -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: geneXtendeR
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneXtendeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings geneXtendeR_1.6.0.tar.gz
StartedAt: 2018-10-17 02:14:10 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:37:33 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1403.1 seconds
RetCode: 0
Status:  OK  
CheckDir: geneXtendeR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneXtendeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings geneXtendeR_1.6.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/geneXtendeR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.0'
* 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 whether package 'geneXtendeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  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
* 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 ... 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-3.7-bioc/R/library/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 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
meanPeakLengthPlot 48.33   1.14   56.03
hotspotPlot        37.47   0.50  133.84
barChart           32.65   0.98   38.16
cumlinePlot        29.42   0.47   33.70
annotate           26.41   0.57   28.87
linePlot           25.48   0.51   39.44
plotWordFreq       24.20   0.36   27.84
makeWordCloud      22.59   0.35  196.29
diffGO             21.36   0.36   43.09
peakLengthBoxplot  20.35   0.31   23.39
makeNetwork        20.16   0.39   24.44
meanPeakLength     18.85   0.25   22.38
distinct           17.69   0.36   24.43
rat                 5.44   0.19    5.62
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
meanPeakLengthPlot 41.96   0.70   54.17
hotspotPlot        40.07   0.46   45.73
barChart           25.77   0.56   29.33
cumlinePlot        25.84   0.31   28.31
linePlot           24.04   0.39   28.49
peakLengthBoxplot  21.59   0.36   24.51
annotate           20.80   0.34   26.69
makeWordCloud      20.73   0.38   26.72
distinct           20.70   0.28   23.08
diffGO             19.56   0.44   22.62
makeNetwork        18.96   0.37   23.62
plotWordFreq       18.92   0.31   22.36
meanPeakLength     16.57   0.14   44.03
* 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-3.7-bioc/meat/geneXtendeR.Rcheck/00check.log'
for details.

Installation output

geneXtendeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/geneXtendeR_1.6.0.tar.gz && rm -rf geneXtendeR.buildbin-libdir && mkdir geneXtendeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneXtendeR.buildbin-libdir geneXtendeR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL geneXtendeR_1.6.0.zip && rm geneXtendeR_1.6.0.tar.gz geneXtendeR_1.6.0.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 6938k  100 6938k    0     0  51.8M      0 --:--:-- --:--:-- --:--:-- 54.6M

install for i386

* installing *source* package 'geneXtendeR' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c annotate.c -o annotate.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/geneXtendeR.buildbin-libdir/geneXtendeR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geneXtendeR'
    finding HTML links ... done
    allPeakLengths                          html  
    annotate                                html  
    barChart                                html  
    cumlinePlot                             html  
    diffGO                                  html  
    distinct                                html  
    hotspotPlot                             html  
    linePlot                                html  
    makeNetwork                             html  
    makeWordCloud                           html  
    meanPeakLength                          html  
    meanPeakLengthPlot                      html  
    peakLengthBoxplot                       html  
    peaksInput                              html  
    peaksMerge                              html  
    plotWordFreq                            html  
    rat                                     html  
    samplepeaksinput                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'geneXtendeR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c annotate.c -o annotate.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/geneXtendeR.buildbin-libdir/geneXtendeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneXtendeR' as geneXtendeR_1.6.0.zip
* DONE (geneXtendeR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'geneXtendeR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

geneXtendeR.Rcheck/examples_i386/geneXtendeR-Ex.timings

nameusersystemelapsed
allPeakLengths0.030.040.33
annotate26.41 0.5728.87
barChart32.65 0.9838.16
cumlinePlot29.42 0.4733.70
diffGO21.36 0.3643.09
distinct17.69 0.3624.43
hotspotPlot 37.47 0.50133.84
linePlot25.48 0.5139.44
makeNetwork20.16 0.3924.44
makeWordCloud 22.59 0.35196.29
meanPeakLength18.85 0.2522.38
meanPeakLengthPlot48.33 1.1456.03
peakLengthBoxplot20.35 0.3123.39
peaksInput0.350.081.59
peaksMerge0.30.00.3
plotWordFreq24.20 0.3627.84
rat5.440.195.62
samplepeaksinput0.020.000.02

geneXtendeR.Rcheck/examples_x64/geneXtendeR-Ex.timings

nameusersystemelapsed
allPeakLengths0.030.000.03
annotate20.80 0.3426.69
barChart25.77 0.5629.33
cumlinePlot25.84 0.3128.31
diffGO19.56 0.4422.62
distinct20.70 0.2823.08
hotspotPlot40.07 0.4645.73
linePlot24.04 0.3928.49
makeNetwork18.96 0.3723.62
makeWordCloud20.73 0.3826.72
meanPeakLength16.57 0.1444.03
meanPeakLengthPlot41.96 0.7054.17
peakLengthBoxplot21.59 0.3624.51
peaksInput0.240.030.27
peaksMerge0.390.000.41
plotWordFreq18.92 0.3122.36
rat4.750.184.92
samplepeaksinput0.010.000.01