Back to Multiple platform build/check report for BioC 3.7
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

CHECK report for LowMACA on tokay2

This page was generated on 2018-10-17 08:40:14 -0400 (Wed, 17 Oct 2018).

Package 801/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LowMACA 1.12.0
Stefano de Pretis , Giorgio Melloni
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/LowMACA
Branch: RELEASE_3_7
Last Commit: c9c3a67
Last Changed Date: 2018-04-30 10:35:36 -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 [ WARNINGS ] 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: LowMACA
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LowMACA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings LowMACA_1.12.0.tar.gz
StartedAt: 2018-10-17 03:00:03 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:26:13 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1569.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: LowMACA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LowMACA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings LowMACA_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/LowMACA.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 'LowMACA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LowMACA' version '1.12.0'
* 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-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/LowMACA-class.Rd:62: file link 'AAMultipleAlignment' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/LowMACA-class.Rd:71: file link 'getMutationData' in package 'cgdsr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/allPfamAnalysis.Rd:52: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/allPfamAnalysis.Rd:54: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/getMutations.Rd:20: file link 'getMutationData' in package 'cgdsr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/getMutations.Rd:32: file link 'getMutationData' in package 'cgdsr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/lfmSingleSequence.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/lfmSingleSequence.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/showTumorType.Rd:19: file link 'getCancerStudies' in package 'cgdsr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/showTumorType.Rd:26: file link 'getCancerStudies' in package 'cgdsr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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      180.92   3.74  196.89
setup                 77.09  24.44  160.44
lfmSingleSequence     93.97   2.09  102.19
LowMACA-class         40.70  14.57   86.19
LowMACA-package       23.94   7.30   47.53
getMutations           7.47   2.17   15.08
lmPlotSingleSequence   3.62   0.18   10.04
alignSequences         3.47   0.14   29.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
allPfamAnalysis      187.90   3.96  204.17
lfmSingleSequence     95.11   2.19  103.28
setup                 50.61  24.11  123.44
LowMACA-class         28.01  10.81   66.45
LowMACA-package       18.41   6.22   40.97
getMutations           5.34   1.81   14.72
alignSequences         3.60   0.05   27.58
lmPlotSingleSequence   2.78   0.18    9.81
* 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-3.7-bioc/meat/LowMACA.Rcheck/00check.log'
for details.

Installation output

LowMACA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/LowMACA_1.12.0.tar.gz && rm -rf LowMACA.buildbin-libdir && mkdir LowMACA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LowMACA.buildbin-libdir LowMACA_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL LowMACA_1.12.0.zip && rm LowMACA_1.12.0.tar.gz LowMACA_1.12.0.zip
###
##############################################################################
##############################################################################


  % 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  108k  100  108k    0     0  1913k      0 --:--:-- --:--:-- --:--:-- 2178k

install for i386

* installing *source* package 'LowMACA' ...
** R
** data
** inst
** byte-compile and prepare 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-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/LowMACA-class.Rd:62: file link 'AAMultipleAlignment' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/LowMACA-class.Rd:71: file link 'getMutationData' in package 'cgdsr' does not exist and so has been treated as a topic
    LowMACA-package                         html  
    LowMACA_AML                             html  
    alignSequences                          html  
    allPfamAnalysis                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/allPfamAnalysis.Rd:52: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/allPfamAnalysis.Rd:54: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    bpAll                                   html  
    entropy                                 html  
    getMutations                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/getMutations.Rd:20: file link 'getMutationData' in package 'cgdsr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/getMutations.Rd:32: file link 'getMutationData' in package 'cgdsr' does not exist and so has been treated as a topic
    lfm                                     html  
    lfmSingleSequence                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/lfmSingleSequence.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/lfmSingleSequence.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    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-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/showTumorType.Rd:19: file link 'getCancerStudies' in package 'cgdsr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyaagpE/R.INSTALL20585497385/LowMACA/man/showTumorType.Rd:26: file link 'getCancerStudies' in package 'cgdsr' does not exist and so has been treated as a topic
** 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_1.12.0.zip
* DONE (LowMACA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'LowMACA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

LowMACA.Rcheck/examples_i386/LowMACA-Ex.timings

nameusersystemelapsed
BLOSUM620.030.000.03
LowMACA-class40.7014.5786.19
LowMACA-package23.94 7.3047.53
LowMACA_AML0.060.000.06
alignSequences 3.47 0.1429.39
allPfamAnalysis180.92 3.74196.89
bpAll0.810.010.83
entropy0.780.020.79
getMutations 7.47 2.1715.08
lfm1.810.051.86
lfmSingleSequence 93.97 2.09102.19
lmAlignment0.050.000.05
lmEntropy0.870.020.89
lmMutations0.050.010.06
lmObj0.110.020.12
lmParams0.910.011.36
lmPlot1.470.031.50
lmPlotSingleSequence 3.62 0.1810.04
mapMutations0.750.030.78
newLowMACA3.530.063.59
nullProfile0.850.000.84
parallelize0.640.000.64
protter1.140.003.16
setup 77.09 24.44160.44
showTumorType0.310.170.80

LowMACA.Rcheck/examples_x64/LowMACA-Ex.timings

nameusersystemelapsed
BLOSUM620.020.000.02
LowMACA-class28.0110.8166.45
LowMACA-package18.41 6.2240.97
LowMACA_AML0.040.000.05
alignSequences 3.60 0.0527.58
allPfamAnalysis187.90 3.96204.17
bpAll0.990.000.98
entropy1.300.021.31
getMutations 5.34 1.8114.72
lfm1.930.031.95
lfmSingleSequence 95.11 2.19103.28
lmAlignment0.040.020.07
lmEntropy0.850.010.85
lmMutations0.090.001.71
lmObj0.170.020.19
lmParams0.690.011.14
lmPlot1.780.001.78
lmPlotSingleSequence2.780.189.81
mapMutations0.580.000.58
newLowMACA3.200.033.23
nullProfile1.140.031.17
parallelize0.540.000.54
protter0.870.013.10
setup 50.61 24.11123.44
showTumorType0.250.110.67