ASpli 0.99.13
Estefania Mancini
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ASpli | | Last Changed Rev: 120349 / Revision: 121152 | | Last Changed Date: 2016-08-22 12:49:16 -0700 (Mon, 22 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf ASpli.buildbin-libdir ASpli.Rcheck && mkdir ASpli.buildbin-libdir ASpli.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ASpli.buildbin-libdir ASpli_0.99.13.tar.gz >ASpli.Rcheck\00install.out 2>&1 && cp ASpli.Rcheck\00install.out ASpli-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ASpli.buildbin-libdir --install="check:ASpli-install.out" --force-multiarch --no-vignettes --timings ASpli_0.99.13.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/ASpli.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ASpli/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASpli' version '0.99.13'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'GenomicRanges' 'GenomicFeatures' 'edgeR' 'BiocGenerics' 'IRanges'
'GenomicAlignments' 'DESeq2' 'DEXSeq' 'Gviz' 'S4Vectors'
'AnnotationDbi' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'ASpli' 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
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readCounts,ASpliFeatures: no visible binding for global variable
'targets'
Undefined global functions or variables:
targets
* 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 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
DUreport_DEXSeq 143.83 3.48 147.33
ASpli-package 102.79 4.78 109.06
acc_AS 98.82 2.89 101.84
plotTopTags 96.55 3.02 99.62
AsDiscover-methods 91.76 3.63 95.41
acc_DU 84.95 2.85 88.53
DUreport 79.80 3.04 82.86
acc_counts 79.14 2.97 82.10
readCounts 77.51 2.90 80.51
loadBAM 15.38 0.32 15.69
binGenome 11.78 0.03 11.81
acc_features 10.96 0.04 11.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DUreport_DEXSeq 132.83 3.18 141.00
ASpli-package 114.65 5.33 121.47
plotTopTags 91.15 1.67 92.82
AsDiscover-methods 87.72 5.10 92.86
acc_AS 85.16 2.59 87.75
readCounts 76.63 2.03 79.16
DUreport 74.27 3.44 80.70
acc_DU 74.42 1.35 75.77
acc_counts 70.04 1.81 71.90
loadBAM 13.46 0.31 13.77
binGenome 12.56 0.03 12.59
acc_features 12.31 0.04 12.34
* 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 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/ASpli.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ASpli' ...
** 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 'ASpli' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASpli' as ASpli_0.99.13.zip
* DONE (ASpli)