Package: flagme

Version: 1.38.1

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_1.38.1.tar.gz

StartedAt: 2019-04-15 23:55:57 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-16 00:06:25 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 627.7 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_1.38.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flagme.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.38.1’
* 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  53.533  2.381  56.308
peaksAlignment       40.846  1.659  42.859
corPrt               39.825  1.697  41.730
ndpRT                39.175  1.658  41.198
dynRT                38.878  1.522  40.690
plotSpectra          36.616  1.875  38.695
retFatMatrix         23.408  0.738  24.323
imputePeaks          12.242  0.378  12.701
addXCMSPeaks         11.499  0.403  11.952
plot                 11.442  0.421  11.966
calcTimeDiffs         9.229  0.608   9.881
rmaFitUnit            8.860  0.536   9.471
multipleAlignment     8.683  0.211   8.985
dp                    8.541  0.258   9.013
progressiveAlignment  8.301  0.303   8.655
gatherInfo            7.760  0.295   8.121
peaksDataset          7.494  0.251   7.822
normDotProduct        7.321  0.267   7.633
clusterAlignment      7.222  0.222   7.466
compress              6.787  0.182   6.983
addAMDISPeaks         5.903  0.282   6.223
* 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-3.8-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	5.903	0.282	6.223
addChromaTOFPeaks	4.706	0.195	4.921
addXCMSPeaks	11.499	0.403	11.952
betweenAlignment	0.000	0.000	0.001
calcTimeDiffs	9.229	0.608	9.881
clusterAlignment	7.222	0.222	7.466
compress	6.787	0.182	6.983
corPrt	39.825	1.697	41.730
dp	8.541	0.258	9.013
dynRT	38.878	1.522	40.690
gatherInfo	7.760	0.295	8.121
imputePeaks	12.242	0.378	12.701
multipleAlignment	8.683	0.211	8.985
ndpRT	39.175	1.658	41.198
normDotProduct	7.321	0.267	7.633
parseChromaTOF	4.169	0.015	4.210
parseELU	3.641	0.012	3.701
peaksAlignment	40.846	1.659	42.859
peaksDataset	7.494	0.251	7.822
plot	11.442	0.421	11.966
plotImage	4.740	0.197	4.982
plotMultipleSpectra	53.533	2.381	56.308
plotSpectra	36.616	1.875	38.695
progressiveAlignment	8.301	0.303	8.655
retFatMatrix	23.408	0.738	24.323
rmaFitUnit	8.860	0.536	9.471