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BioC 3.5: CHECK report for SplicingGraphs on tokay2

This page was generated on 2017-08-16 13:22:20 -0400 (Wed, 16 Aug 2017).

Package 1260/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SplicingGraphs 1.16.0
H. Pagès
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/SplicingGraphs
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SplicingGraphs
Version: 1.16.0
Command: rm -rf SplicingGraphs.buildbin-libdir SplicingGraphs.Rcheck && mkdir SplicingGraphs.buildbin-libdir SplicingGraphs.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SplicingGraphs.buildbin-libdir SplicingGraphs_1.16.0.tar.gz >SplicingGraphs.Rcheck\00install.out 2>&1 && cp SplicingGraphs.Rcheck\00install.out SplicingGraphs-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SplicingGraphs.buildbin-libdir --install="check:SplicingGraphs-install.out" --force-multiarch --no-vignettes --timings SplicingGraphs_1.16.0.tar.gz
StartedAt: 2017-08-16 03:06:04 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:16:14 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 610.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SplicingGraphs.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SplicingGraphs.buildbin-libdir SplicingGraphs.Rcheck && mkdir SplicingGraphs.buildbin-libdir SplicingGraphs.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SplicingGraphs.buildbin-libdir SplicingGraphs_1.16.0.tar.gz >SplicingGraphs.Rcheck\00install.out 2>&1 && cp SplicingGraphs.Rcheck\00install.out SplicingGraphs-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SplicingGraphs.buildbin-libdir --install="check:SplicingGraphs-install.out" --force-multiarch --no-vignettes --timings SplicingGraphs_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SplicingGraphs.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SplicingGraphs/DESCRIPTION' ... OK
* this is package 'SplicingGraphs' version '1.16.0'
* 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 'SplicingGraphs' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
  Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SplicingGraphs.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'GenomicFeatures' 'GenomicAlignments' 'Rgraphviz' 'igraph'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to 'igraph' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
  'S4Vectors:::matchIntegerPairs' 'S4Vectors:::orderIntegerPairs'
  'S4Vectors:::selfmatchIntegerPairs'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'GenomicAlignments:::fillJunctionGaps'
  'GenomicFeatures:::.collapse_df' 'IRanges:::newCompressedList0'
  'IRanges:::regroupBySupergroup' 'S4Vectors:::setPrototypeFromObject'
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Undocumented code objects:
  'reportReads'
Undocumented S4 methods:
  generic '[' and siglist 'SplicingGraphs,ANY,ANY,ANY'
  generic 'reportReads' and siglist 'SplicingGraphs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'countReads-methods':
  'reportReads'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
plotTranscripts-methods 25.10   0.11   25.43
toy_data                13.39   0.00   13.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plotTranscripts-methods 29.41   0.06   29.62
toy_data                17.11   0.00   17.11
countReads-methods       5.92   0.02    5.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* 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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/SplicingGraphs.Rcheck/00check.log'
for details.


SplicingGraphs.Rcheck/00install.out:


install for i386

* installing *source* package 'SplicingGraphs' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'

install for x64

* installing *source* package 'SplicingGraphs' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
* MD5 sums
packaged installation of 'SplicingGraphs' as SplicingGraphs_1.16.0.zip
* DONE (SplicingGraphs)

SplicingGraphs.Rcheck/examples_i386/SplicingGraphs-Ex.timings:

nameusersystemelapsed
SplicingGraphs-class2.560.002.56
SplicingGraphs-package000
assignReads3.400.003.42
bubbles-methods2.130.002.12
countReads-methods4.090.004.10
plotTranscripts-methods25.10 0.1125.43
rsgedgesByGene-methods2.270.002.27
sgedges-methods2.870.002.87
sgedgesByGene-methods2.140.032.17
sgraph-methods1.210.001.21
toy_data13.39 0.0013.39
txpath-methods2.350.032.38

SplicingGraphs.Rcheck/examples_x64/SplicingGraphs-Ex.timings:

nameusersystemelapsed
SplicingGraphs-class3.550.003.54
SplicingGraphs-package000
assignReads4.190.004.21
bubbles-methods2.980.002.98
countReads-methods5.920.025.94
plotTranscripts-methods29.41 0.0629.62
rsgedgesByGene-methods3.220.053.27
sgedges-methods3.650.003.66
sgedgesByGene-methods2.430.012.43
sgraph-methods1.450.021.47
toy_data17.11 0.0017.11
txpath-methods3.310.003.31