Package: flagme

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flagme_1.36.0.tar.gz

StartedAt: 2018-10-16 21:21:42 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:30:53 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 550.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flagme.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flagme_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/flagme.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.36.0’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘gcspikelite’
* 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 ‘flagme’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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 ... WARNING
plotMultipleSpectra.Rd: non-ASCII input and no declared encoding
problem found in ‘plotMultipleSpectra.Rd’
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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
plotMultipleSpectra  48.823  2.240  51.430
plotSpectra          35.166  1.675  37.113
peaksAlignment       34.363  1.504  36.076
ndpRT                33.343  1.454  34.950
dynRT                31.233  1.610  32.980
corPrt               30.697  1.588  32.340
retFatMatrix         20.045  0.674  20.872
imputePeaks          11.579  0.322  11.976
plot                 10.212  0.340  10.630
addXCMSPeaks         10.100  0.319  10.458
rmaFitUnit            8.059  0.505   8.615
calcTimeDiffs         7.135  0.535   7.686
progressiveAlignment  7.398  0.245   7.683
multipleAlignment     7.157  0.176   7.384
compress              6.668  0.190   6.882
gatherInfo            6.526  0.295   6.856
normDotProduct        6.354  0.232   6.610
clusterAlignment      6.156  0.307   6.487
peaksDataset          6.144  0.238   6.425
dp                    6.023  0.260   6.300
addAMDISPeaks         4.861  0.294   5.179
* 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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/flagme.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flagme
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flagme’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dp.c -o dp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pearson.c -o pearson.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/flagme/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘flagme.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
* DONE (flagme)

name	user	system	elapsed
addAMDISPeaks	4.861	0.294	5.179
addChromaTOFPeaks	4.114	0.123	4.248
addXCMSPeaks	10.100	0.319	10.458
betweenAlignment	0.001	0.000	0.001
calcTimeDiffs	7.135	0.535	7.686
clusterAlignment	6.156	0.307	6.487
compress	6.668	0.190	6.882
corPrt	30.697	1.588	32.340
dp	6.023	0.260	6.300
dynRT	31.233	1.610	32.980
gatherInfo	6.526	0.295	6.856
imputePeaks	11.579	0.322	11.976
multipleAlignment	7.157	0.176	7.384
ndpRT	33.343	1.454	34.950
normDotProduct	6.354	0.232	6.610
parseChromaTOF	3.943	0.017	3.988
parseELU	3.265	0.010	3.295
peaksAlignment	34.363	1.504	36.076
peaksDataset	6.144	0.238	6.425
plot	10.212	0.340	10.630
plotImage	3.896	0.197	4.111
plotMultipleSpectra	48.823	2.240	51.430
plotSpectra	35.166	1.675	37.113
progressiveAlignment	7.398	0.245	7.683
retFatMatrix	20.045	0.674	20.872
rmaFitUnit	8.059	0.505	8.615