BioC 3.3: CHECK report for LowMACA on linux2.bioconductor.org

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

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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

* 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)

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