BioC 3.2: CHECK report for bsseq on windows1.bioconductor.org
This page was generated on 2015-10-27 17:30:02 -0400 (Tue, 27 Oct 2015).
bsseq 1.6.0
Kasper Daniel Hansen
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/bsseq | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
| Package: bsseq
|
| Version: 1.6.0
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| Command: rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.6.0.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.6.0.tar.gz
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| StartedAt: 2015-10-27 00:12:24 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 00:15:30 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 186.1 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: bsseq.Rcheck
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| Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.6.0.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.6.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/bsseq.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bsseq/DESCRIPTION' ... OK
* this is package 'bsseq' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics' 'IRanges' 'GenomicRanges' 'SummarizedExperiment'
'parallel' 'GenomeInfoDb'
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 'bsseq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
data 5.0Mb
* 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [18s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
BSmooth.tstat 4.9 0.7 6.15
** running examples for arch 'x64' ... [19s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
BSmooth.tstat 5.5 0.65 6.15
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [6s]
[8s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [7s]
[8s] 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 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/bsseq.Rcheck/00check.log'
for details.
bsseq.Rcheck/00install.out:
install for i386
* installing *source* package 'bsseq' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'bsseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bsseq' as bsseq_1.6.0.zip
* DONE (bsseq)
bsseq.Rcheck/examples_i386/bsseq-Ex.timings:
| name | user | system | elapsed
|
| BS.chr22 | 0.79 | 0.03 | 0.83 |
|
| BSmooth | 0 | 0 | 0 |
|
| BSmooth.tstat | 4.90 | 0.70 | 6.15 |
|
| BSseq-class | 0.13 | 0.00 | 0.12 |
|
| BSseq | 0.08 | 0.00 | 0.08 |
|
| data.frame2GRanges | 0.01 | 0.00 | 0.01 |
|
| dmrFinder | 1.55 | 0.16 | 1.77 |
|
| fisherTests | 0.06 | 0.00 | 0.06 |
|
| getCoverage | 0.34 | 0.05 | 0.39 |
|
| getMeth | 1.38 | 0.45 | 1.83 |
|
| getStats | 0.51 | 0.08 | 0.59 |
|
| goodnessOfFit | 2.03 | 0.16 | 2.22 |
|
| hasGRanges-class | 0 | 0 | 0 |
|
| read.bismark | 0.07 | 0.00 | 0.06 |
|
| read.umtab | 0 | 0 | 0 |
|
bsseq.Rcheck/examples_x64/bsseq-Ex.timings:
| name | user | system | elapsed
|
| BS.chr22 | 1.30 | 0.07 | 1.36 |
|
| BSmooth | 0 | 0 | 0 |
|
| BSmooth.tstat | 5.50 | 0.65 | 6.15 |
|
| BSseq-class | 0.14 | 0.00 | 0.14 |
|
| BSseq | 0.11 | 0.00 | 0.11 |
|
| data.frame2GRanges | 0.02 | 0.00 | 0.02 |
|
| dmrFinder | 1.45 | 0.14 | 1.59 |
|
| fisherTests | 0.09 | 0.02 | 0.11 |
|
| getCoverage | 0.49 | 0.09 | 0.58 |
|
| getMeth | 0.98 | 0.39 | 1.38 |
|
| getStats | 0.39 | 0.04 | 0.42 |
|
| goodnessOfFit | 1.88 | 0.26 | 2.14 |
|
| hasGRanges-class | 0 | 0 | 0 |
|
| read.bismark | 0.07 | 0.00 | 0.07 |
|
| read.umtab | 0 | 0 | 0 |
|