SplicingGraphs 1.10.0
H. Pages
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SplicingGraphs | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SplicingGraphs.buildbin-libdir SplicingGraphs_1.10.0.tar.gz >SplicingGraphs.Rcheck\00install.out 2>&1 && cp SplicingGraphs.Rcheck\00install.out SplicingGraphs-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SplicingGraphs.buildbin-libdir --install="check:SplicingGraphs-install.out" --force-multiarch --no-vignettes --timings SplicingGraphs_1.10.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/SplicingGraphs.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.10.0'
* 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 'SplicingGraphs' can be installed ... OK
* 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.
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'GenomicAlignments:::fillJunctionGaps'
'GenomicFeatures:::.collapse_df' 'IRanges:::newCompressedList0'
'IRanges:::regroupBySupergroup' 'S4Vectors:::matchIntegerPairs'
'S4Vectors:::orderIntegerPairs' 'S4Vectors:::selfmatchIntegerPairs'
'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 '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' ... [150s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 42.38 0.1 43.29
toy_data 21.85 0.0 21.85
countReads-methods 7.47 0.0 7.49
sgedges-methods 5.85 0.0 5.85
** running examples for arch 'x64' ... [162s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 44.57 0.05 44.62
toy_data 25.50 0.00 25.59
countReads-methods 7.43 0.02 7.44
sgedges-methods 5.84 0.00 5.84
rsgedgesByGene-methods 5.47 0.00 6.44
txpath-methods 4.70 0.00 5.71
bubbles-methods 3.82 0.01 5.26
assignReads 3.77 0.00 5.86
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R' [17s]
[18s] OK
** running tests for arch 'x64' ...
Running 'run_unitTests.R' [19s]
[20s] 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: 2 WARNINGs, 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/SplicingGraphs.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'SplicingGraphs' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'SplicingGraphs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SplicingGraphs' as SplicingGraphs_1.10.0.zip
* DONE (SplicingGraphs)