BioC 3.6: CHECK report for LowMACA on veracruz1

Package: LowMACA

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.9.0.tar.gz

StartedAt: 2017-08-16 04:57:22 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:08:23 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 660.8 seconds

RetCode: 0

Status:  OK

CheckDir: LowMACA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/LowMACA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.9.0’
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
allPfamAnalysis      152.679  4.098 161.250
lfmSingleSequence     81.192  2.065  85.515
LowMACA-class         10.738  0.939  40.335
setup                  7.508  2.760  68.648
LowMACA-package        9.017  0.757  29.817
alignSequences         5.535  3.408  20.198
lmPlotSingleSequence   4.998  0.661   5.976
lmPlot                 4.226  0.696   5.207
getMutations           0.770  0.057   8.367
* 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	0.007	0.002	0.008
LowMACA-class	10.738	0.939	40.335
LowMACA-package	9.017	0.757	29.817
LowMACA_AML	0.025	0.005	0.030
alignSequences	5.535	3.408	20.198
allPfamAnalysis	152.679	4.098	161.250
bpAll	1.327	0.032	1.382
entropy	1.341	0.028	1.388
getMutations	0.770	0.057	8.367
lfm	1.835	0.048	1.926
lfmSingleSequence	81.192	2.065	85.515
lmAlignment	0.052	0.008	0.061
lmEntropy	1.121	0.041	1.185
lmMutations	0.045	0.010	0.056
lmObj	0.099	0.009	0.108
lmParams	0.607	0.025	0.648
lmPlot	4.226	0.696	5.207
lmPlotSingleSequence	4.998	0.661	5.976
mapMutations	0.459	0.014	0.485
newLowMACA	3.095	0.092	3.279
nullProfile	1.300	0.041	1.383
parallelize	0.516	0.014	0.544
protter	1.234	0.032	3.709
setup	7.508	2.760	68.648
showTumorType	0.040	0.008	0.266