BioC 3.3: CHECK report for LowMACA on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:54 -0400 (Tue, 27 Oct 2015).
LowMACA 1.3.0
Stefano de Pretis , Giorgio Melloni
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LowMACA | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
Summary
| Package: LowMACA |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings LowMACA_1.3.0.tar.gz |
| StartedAt: 2015-10-27 05:18:31 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 05:27:04 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 513.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LowMACA.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings LowMACA_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/LowMACA.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LowMACA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LowMACA’ version ‘1.3.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘LowMACA’ can be installed ... [16s/17s] 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
* 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 ... 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 ... [361s/357s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
allPfamAnalysis 174.004 17.213 165.831
lfmSingleSequence 93.286 8.445 90.069
LowMACA-class 11.374 1.429 19.071
LowMACA-package 7.526 1.426 12.248
lmPlotSingleSequence 5.364 1.323 5.374
setup 5.635 0.418 24.911
lmPlot 4.493 1.128 5.590
alignSequences 5.127 0.295 12.207
* 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: OK
LowMACA.Rcheck/00install.out:
* installing *source* package ‘LowMACA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
* DONE (LowMACA)
LowMACA.Rcheck/LowMACA-Ex.timings:
| name | user | system | elapsed
|
| BLOSUM62 | 0.010 | 0.000 | 0.011 |
|
| LowMACA-class | 11.374 | 1.429 | 19.071 |
|
| LowMACA-package | 7.526 | 1.426 | 12.248 |
|
| LowMACA_AML | 0.024 | 0.004 | 0.028 |
|
| alignSequences | 5.127 | 0.295 | 12.207 |
|
| allPfamAnalysis | 174.004 | 17.213 | 165.831 |
|
| bpAll | 1.449 | 0.251 | 1.181 |
|
| entropy | 1.089 | 0.156 | 1.191 |
|
| getMutations | 0.533 | 0.096 | 1.717 |
|
| lfm | 2.665 | 0.264 | 1.940 |
|
| lfmSingleSequence | 93.286 | 8.445 | 90.069 |
|
| lmAlignment | 0.060 | 0.000 | 0.063 |
|
| lmEntropy | 1.456 | 0.247 | 1.288 |
|
| lmMutations | 0.029 | 0.004 | 0.033 |
|
| lmObj | 0.068 | 0.004 | 0.073 |
|
| lmParams | 0.512 | 0.091 | 0.602 |
|
| lmPlot | 4.493 | 1.128 | 5.590 |
|
| lmPlotSingleSequence | 5.364 | 1.323 | 5.374 |
|
| mapMutations | 0.458 | 0.004 | 0.462 |
|
| newLowMACA | 2.890 | 0.048 | 2.940 |
|
| nullProfile | 1.636 | 0.240 | 1.477 |
|
| parallelize | 0.744 | 0.004 | 0.751 |
|
| protter | 1.131 | 0.168 | 1.768 |
|
| setup | 5.635 | 0.418 | 24.911 |
|
| showTumorType | 0.025 | 0.028 | 0.096 |
|