SplicingGraphs 1.16.1
H. Pagès
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/SplicingGraphs | | Branch: RELEASE_3_5 | | Last Commit: 788b154 | | Last Changed Date: 2017-10-03 21:07:00 -0400 (Tue, 03 Oct 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### 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_1.16.1.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_1.16.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SplicingGraphs.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.16.1'
* 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 '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 25.83 0.15 26.06
toy_data 11.56 0.00 11.56
countReads-methods 6.60 0.00 6.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 29.18 0.12 29.39
toy_data 16.22 0.00 16.22
countReads-methods 5.21 0.00 5.20
* 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.
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_1.16.1.zip
* DONE (SplicingGraphs)