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CHECK report for LowMACA on tokay1

This page was generated on 2018-04-05 14:38:20 -0400 (Thu, 05 Apr 2018).

Package 758/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LowMACA 1.10.0
Stefano de Pretis , Giorgio Melloni
Snapshot Date: 2018-04-04 16:45:02 -0400 (Wed, 04 Apr 2018)
URL: https://git.bioconductor.org/packages/LowMACA
Branch: RELEASE_3_6
Last Commit: 1f18a12
Last Changed Date: 2017-10-30 12:40:50 -0400 (Mon, 30 Oct 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 [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  ERROR  OK 

Summary

Package: LowMACA
Version: 1.10.0
Command: rm -rf LowMACA.buildbin-libdir LowMACA.Rcheck && mkdir LowMACA.buildbin-libdir LowMACA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LowMACA.buildbin-libdir LowMACA_1.10.0.tar.gz >LowMACA.Rcheck\00install.out 2>&1 && cp LowMACA.Rcheck\00install.out LowMACA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=LowMACA.buildbin-libdir --install="check:LowMACA-install.out" --force-multiarch --no-vignettes --timings LowMACA_1.10.0.tar.gz
StartedAt: 2018-04-05 01:07:43 -0400 (Thu, 05 Apr 2018)
EndedAt: 2018-04-05 01:27:41 -0400 (Thu, 05 Apr 2018)
EllapsedTime: 1198.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: LowMACA.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf LowMACA.buildbin-libdir LowMACA.Rcheck && mkdir LowMACA.buildbin-libdir LowMACA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LowMACA.buildbin-libdir LowMACA_1.10.0.tar.gz >LowMACA.Rcheck\00install.out 2>&1 && cp LowMACA.Rcheck\00install.out LowMACA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=LowMACA.buildbin-libdir --install="check:LowMACA-install.out" --force-multiarch --no-vignettes --timings LowMACA_1.10.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/LowMACA.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LowMACA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LowMACA' version '1.10.0'
* 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 'LowMACA' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/LowMACA-class.Rd:62: missing file link 'AAMultipleAlignment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/LowMACA-class.Rd:71: missing file link 'getMutationData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/allPfamAnalysis.Rd:52: missing file link 'BiocParallelParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/allPfamAnalysis.Rd:54: missing file link 'bpparam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/getMutations.Rd:20: missing file link 'getMutationData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/getMutations.Rd:32: missing file link 'getMutationData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/lfmSingleSequence.Rd:29: missing file link 'BiocParallelParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/lfmSingleSequence.Rd:31: missing file link 'bpparam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/showTumorType.Rd:19: missing file link 'getCancerStudies'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/showTumorType.Rd:26: missing file link 'getCancerStudies'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/LowMACA.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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
allPfamAnalysis      174.82   2.47  189.64
lfmSingleSequence     92.89   1.59  100.76
setup                 21.41   5.72   65.47
LowMACA-class         15.44   3.64   40.13
LowMACA-package       10.91   2.13   25.61
alignSequences         3.83   0.07   24.04
getMutations           2.39   0.60    6.32
lmPlotSingleSequence   2.53   0.09    7.73
lmPlot                 1.74   0.06    6.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
allPfamAnalysis      147.22   2.31  161.15
lfmSingleSequence     82.12   1.47   89.24
setup                 17.86   7.62   62.22
LowMACA-class         15.97   4.03   38.62
LowMACA-package        9.48   2.00   23.75
lmPlotSingleSequence   3.11   0.13    8.33
alignSequences         2.97   0.07   15.91
lmPlot                 2.33   0.04    7.77
getMutations           1.76   0.41    5.34
* 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
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/LowMACA.Rcheck/00check.log'
for details.

Installation output

LowMACA.Rcheck/00install.out


install for i386

* installing *source* package 'LowMACA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'LowMACA'
    finding HTML links ... done
    BLOSUM62                                html  
    LowMACA-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/LowMACA-class.Rd:62: missing file link 'AAMultipleAlignment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/LowMACA-class.Rd:71: missing file link 'getMutationData'
    LowMACA-package                         html  
    LowMACA_AML                             html  
    alignSequences                          html  
    allPfamAnalysis                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/allPfamAnalysis.Rd:52: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/allPfamAnalysis.Rd:54: missing file link 'bpparam'
    bpAll                                   html  
    entropy                                 html  
    getMutations                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/getMutations.Rd:20: missing file link 'getMutationData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/getMutations.Rd:32: missing file link 'getMutationData'
    lfm                                     html  
    lfmSingleSequence                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/lfmSingleSequence.Rd:29: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/lfmSingleSequence.Rd:31: missing file link 'bpparam'
    lmAlignment                             html  
    lmEntropy                               html  
    lmMutations                             html  
    lmObj                                   html  
    lmParams                                html  
    lmPlot                                  html  
    lmPlotSingleSequence                    html  
    mapMutations                            html  
    newLowMACA                              html  
    nullProfile                             html  
    parallelize                             html  
    protter                                 html  
    setup                                   html  
    showTumorType                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/showTumorType.Rd:19: missing file link 'getCancerStudies'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgN7kgJ/R.INSTALL1694235f16dd/LowMACA/man/showTumorType.Rd:26: missing file link 'getCancerStudies'
** building package indices
** installing vignettes
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
In R CMD INSTALL

install for x64

* installing *source* package 'LowMACA' ...
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
* MD5 sums
packaged installation of 'LowMACA' as LowMACA_1.10.0.zip
* DONE (LowMACA)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

LowMACA.Rcheck/examples_i386/LowMACA-Ex.timings

nameusersystemelapsed
BLOSUM620.010.000.01
LowMACA-class15.44 3.6440.13
LowMACA-package10.91 2.1325.61
LowMACA_AML0.030.020.04
alignSequences 3.83 0.0724.04
allPfamAnalysis174.82 2.47189.64
bpAll1.250.001.25
entropy1.220.001.22
getMutations2.390.606.32
lfm2.100.032.13
lfmSingleSequence 92.89 1.59100.76
lmAlignment0.060.000.07
lmEntropy1.20.01.2
lmMutations0.050.020.06
lmObj0.080.010.10
lmParams0.590.021.04
lmPlot1.740.066.94
lmPlotSingleSequence2.530.097.73
mapMutations0.590.000.60
newLowMACA3.210.073.26
nullProfile1.290.001.30
parallelize0.610.000.61
protter1.440.003.53
setup21.41 5.7265.47
showTumorType0.250.070.61

LowMACA.Rcheck/examples_x64/LowMACA-Ex.timings

nameusersystemelapsed
BLOSUM62000
LowMACA-class15.97 4.0338.62
LowMACA-package 9.48 2.0023.75
LowMACA_AML0.020.000.02
alignSequences 2.97 0.0715.91
allPfamAnalysis147.22 2.31161.15
bpAll1.300.011.32
entropy1.270.001.27
getMutations1.760.415.34
lfm2.270.022.28
lfmSingleSequence82.12 1.4789.24
lmAlignment0.050.000.04
lmEntropy1.340.011.36
lmMutations0.050.000.05
lmObj0.110.000.11
lmParams0.560.021.03
lmPlot2.330.047.77
lmPlotSingleSequence3.110.138.33
mapMutations0.530.010.54
newLowMACA3.170.083.25
nullProfile1.530.001.53
parallelize0.850.020.86
protter1.620.003.75
setup17.86 7.6262.22
showTumorType0.110.070.45