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This page was generated on 2022-04-13 12:06:49 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for maser on tokay2


To the developers/maintainers of the maser package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maser.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1049/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maser 1.12.1  (landing page)
Diogo F.T. Veiga
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/maser
git_branch: RELEASE_3_14
git_last_commit: b243c41
git_last_commit_date: 2022-02-08 08:12:28 -0400 (Tue, 08 Feb 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: maser
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maser.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings maser_1.12.1.tar.gz
StartedAt: 2022-04-12 22:15:16 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 22:23:10 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 474.4 seconds
RetCode: 0
Status:   OK  
CheckDir: maser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maser.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings maser_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/maser.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'maser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'maser' version '1.12.1'
* package encoding: UTF-8
* 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 'maser' can be installed ... OK
* 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 ... NOTE
availableFeaturesUniprotKB: no visible global function definition for
  'read.csv'
availableFeaturesUniprotKB: no visible binding for global variable
  'Category'
availableFeaturesUniprotKB: no visible binding for global variable
  'Name'
filterByIds: no visible binding for global variable 'ID'
mapTranscriptsA3SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsA5SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsMXEevent: no visible global function definition for
  'subjectHits'
mapTranscriptsRIevent: no visible global function definition for
  'subjectHits'
mapTranscriptsSEevent: no visible global function definition for
  'subjectHits'
overlappingFeatures: no visible global function definition for
  'subjectHits'
urlTracksUniprotKB: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  Category ID Name read.csv subjectHits
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotTranscripts            6.96   0.03    6.98
plotUniprotKBFeatures      6.11   0.05    7.00
mapProteinFeaturesToEvents 4.96   0.09    6.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotUniprotKBFeatures      7.16   0.04    8.12
plotTranscripts            7.02   0.03    7.05
mapProteinFeaturesToEvents 5.44   0.07    6.71
* 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-3.14-bioc/meat/maser.Rcheck/00check.log'
for details.



Installation output

maser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/maser_1.12.1.tar.gz && rm -rf maser.buildbin-libdir && mkdir maser.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maser.buildbin-libdir maser_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL maser_1.12.1.zip && rm maser_1.12.1.tar.gz maser_1.12.1.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
 25 1488k   25  374k    0     0   834k      0  0:00:01 --:--:--  0:00:01  833k
100 1488k  100 1488k    0     0  1291k      0  0:00:01  0:00:01 --:--:-- 1292k

install for i386

* installing *source* package 'maser' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'maser'
    finding HTML links ... done
    Maser-class                             html  
    PSI-Maser-character-method              html  
    PSI                                     html  
    annotation-Maser-method                 html  
    availableFeaturesUniprotKB              html  
    boxplot_PSI_levels                      html  
    counts-Maser-method                     html  
    display                                 html  
    dotplot                                 html  
    filterByCoverage                        html  
    filterByEventId                         html  
    geneEvents                              html  
    granges-Maser-method                    html  
    mapProteinFeaturesToEvents              html  
    mapTranscriptsToEvents                  html  
    maser                                   html  
    pca                                     html  
    plotGenePSI                             html  
    plotTranscripts                         html  
    plotUniprotKBFeatures                   html  
    splicingDistribution                    html  
    summary-Maser-method                    html  
    topEvents                               html  
    volcano                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'maser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maser' as maser_1.12.1.zip
* DONE (maser)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'maser' successfully unpacked and MD5 sums checked

Tests output


Example timings

maser.Rcheck/examples_i386/maser-Ex.timings

nameusersystemelapsed
PSI-Maser-character-method0.890.231.28
PSI1.600.091.69
annotation-Maser-method0.540.000.55
availableFeaturesUniprotKB0.100.050.34
boxplot_PSI_levels1.670.752.42
counts-Maser-method0.610.000.61
display1.760.091.97
dotplot1.570.001.56
filterByCoverage1.090.001.09
filterByEventId0.930.000.92
geneEvents1.000.271.27
granges-Maser-method0.680.000.69
mapProteinFeaturesToEvents4.960.096.04
mapTranscriptsToEvents1.890.101.99
maser0.620.000.62
pca1.270.091.36
plotGenePSI2.150.082.24
plotTranscripts6.960.036.98
plotUniprotKBFeatures6.110.057.00
splicingDistribution1.250.031.28
summary-Maser-method0.730.050.78
topEvents0.970.031.00
volcano1.250.011.27

maser.Rcheck/examples_x64/maser-Ex.timings

nameusersystemelapsed
PSI-Maser-character-method0.890.020.91
PSI0.970.041.02
annotation-Maser-method2.070.022.07
availableFeaturesUniprotKB0.070.050.25
boxplot_PSI_levels1.880.011.90
counts-Maser-method0.640.020.65
display2.020.082.10
dotplot1.50.01.5
filterByCoverage1.150.001.15
filterByEventId1.080.001.08
geneEvents1.390.001.39
granges-Maser-method0.840.000.84
mapProteinFeaturesToEvents5.440.076.71
mapTranscriptsToEvents2.060.002.06
maser0.740.000.73
pca1.360.021.39
plotGenePSI2.010.022.05
plotTranscripts7.020.037.05
plotUniprotKBFeatures7.160.048.12
splicingDistribution1.460.001.47
summary-Maser-method0.910.000.91
topEvents1.250.021.26
volcano1.410.001.41