BioC 3.2: CHECK report for LowMACA on oaxaca

Package: LowMACA

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.1.0.tar.gz

StartedAt: 2015-08-24 01:17:09 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:24:35 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 445.7 seconds

RetCode: 0

Status:  OK

CheckDir: LowMACA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/LowMACA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.0’
* 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 ... [24s/37s] 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 ... [71s/185s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
LowMACA-package 10.610  1.266  32.654
LowMACA-class   10.873  0.869  51.203
lmPlot           6.419  0.994   6.858
setup            4.945  0.290  40.784
alignSequences   2.484  0.168  10.453
protter          1.878  0.348   7.844
getMutations     0.826  0.054   9.544
* 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
No methods found in "IRanges" for requests: sapply
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: sapply
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
LowMACA-class	10.873	0.869	51.203
LowMACA-package	10.610	1.266	32.654
alignSequences	2.484	0.168	10.453
bpAll	1.917	0.291	2.056
entropy	1.818	0.489	1.459
getMutations	0.826	0.054	9.544
lfm	0.909	0.031	0.949
lmAlignment	0.064	0.010	0.074
lmEntropy	1.861	0.469	1.626
lmMutations	0.053	0.010	0.064
lmObj	0.109	0.013	0.122
lmParams	0.746	0.039	0.813
lmPlot	6.419	0.994	6.858
mapMutations	0.676	0.025	0.715
newLowMACA	4.140	0.171	4.367
nullProfile	1.969	0.340	1.538
parallelize	0.695	0.030	0.726
protter	1.878	0.348	7.844
setup	4.945	0.290	40.784
showTumorType	0.042	0.012	0.389