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CHECK report for LymphoSeq on tokay1

This page was generated on 2019-04-13 11:26:39 -0400 (Sat, 13 Apr 2019).

Package 856/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LymphoSeq 1.10.0
David Coffey
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/LymphoSeq
Branch: RELEASE_3_8
Last Commit: 255c541
Last Changed Date: 2018-10-30 11:42:01 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LymphoSeq
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LymphoSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings LymphoSeq_1.10.0.tar.gz
StartedAt: 2019-04-13 03:27:33 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:33:19 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 346.5 seconds
RetCode: 0
Status:  OK  
CheckDir: LymphoSeq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LymphoSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings LymphoSeq_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/LymphoSeq.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LymphoSeq/DESCRIPTION' ... OK
* this is package 'LymphoSeq' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'LymphoSeq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cloneTrack    22.13   3.71   25.84
productiveSeq 19.67   1.00   20.67
phyloTree      8.93   0.05    8.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cloneTrack    22.82   1.15   23.97
productiveSeq 20.07   0.81   20.87
phyloTree      5.20   0.00    5.21
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/LymphoSeq.Rcheck/00check.log'
for details.



Installation output

LymphoSeq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/LymphoSeq_1.10.0.tar.gz && rm -rf LymphoSeq.buildbin-libdir && mkdir LymphoSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LymphoSeq.buildbin-libdir LymphoSeq_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL LymphoSeq_1.10.0.zip && rm LymphoSeq_1.10.0.tar.gz LymphoSeq_1.10.0.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  709k  100  709k    0     0  14.8M      0 --:--:-- --:--:-- --:--:-- 16.1M

install for i386

* installing *source* package 'LymphoSeq' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'LymphoSeq'
    finding HTML links ... done
    alignSeq                                html  
    bhattacharyyaCoefficient                html  
    bhattacharyyaMatrix                     html  
    chordDiagramVDJ                         html  
    clonalRelatedness                       html  
    clonality                               html  
    cloneTrack                              html  
    commonSeqs                              html  
    commonSeqsBar                           html  
    commonSeqsPlot                          html  
    commonSeqsVenn                          html  
    differentialAbundance                   html  
    exportFasta                             html  
    geneFreq                                html  
    lorenzCurve                             html  
    mergeFiles                              html  
    pairwisePlot                            html  
    phyloTree                               html  
    productive                              html  
    productiveSeq                           html  
    readImmunoSeq                           html  
    removeSeq                               html  
    searchPublished                         html  
    searchSeq                               html  
    seqMatrix                               html  
    similarityMatrix                        html  
    similarityScore                         html  
    topFreq                                 html  
    topSeqs                                 html  
    topSeqsPlot                             html  
    uniqueSeqs                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'LymphoSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LymphoSeq' as LymphoSeq_1.10.0.zip
* DONE (LymphoSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'LymphoSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

LymphoSeq.Rcheck/examples_i386/LymphoSeq-Ex.timings

nameusersystemelapsed
alignSeq1.150.032.29
bhattacharyyaCoefficient0.160.031.42
bhattacharyyaMatrix0.170.070.25
chordDiagramVDJ0.700.110.82
clonalRelatedness1.660.030.21
clonality0.030.040.07
cloneTrack22.13 3.7125.84
commonSeqs0.150.040.19
commonSeqsBar2.000.292.29
commonSeqsPlot0.390.030.43
commonSeqsVenn0.800.221.01
differentialAbundance3.940.604.53
exportFasta0.250.040.30
geneFreq2.970.053.02
lorenzCurve4.250.004.25
mergeFiles0.170.020.18
pairwisePlot1.120.011.14
phyloTree8.930.058.97
productive0.090.000.10
productiveSeq19.67 1.0020.67
readImmunoSeq0.060.010.08
removeSeq0.100.000.09
searchPublished0.150.070.22
searchSeq101
seqMatrix1.570.091.66
similarityMatrix0.200.030.23
similarityScore0.170.030.20
topFreq2.140.132.27
topSeqs0.170.010.19
topSeqsPlot0.470.050.51
uniqueSeqs0.250.000.25

LymphoSeq.Rcheck/examples_x64/LymphoSeq-Ex.timings

nameusersystemelapsed
alignSeq1.040.031.13
bhattacharyyaCoefficient0.130.040.17
bhattacharyyaMatrix0.20.00.2
chordDiagramVDJ0.700.030.74
clonalRelatedness0.710.020.14
clonality0.040.020.06
cloneTrack22.82 1.1523.97
commonSeqs0.180.000.19
commonSeqsBar1.890.061.95
commonSeqsPlot0.410.000.42
commonSeqsVenn0.810.211.02
differentialAbundance2.220.082.29
exportFasta1.110.001.11
geneFreq1.880.041.92
lorenzCurve1.390.021.41
mergeFiles0.070.000.08
pairwisePlot0.720.000.72
phyloTree5.200.005.21
productive0.060.000.06
productiveSeq20.07 0.8120.87
readImmunoSeq0.040.000.05
removeSeq0.070.020.08
searchPublished0.170.000.17
searchSeq0.720.000.72
seqMatrix2.650.072.73
similarityMatrix0.190.000.19
similarityScore0.170.000.17
topFreq3.890.134.02
topSeqs0.180.000.17
topSeqsPlot0.390.000.39
uniqueSeqs0.210.020.24