Package: flagme

Version: 1.36.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flagme_1.36.0.tar.gz

StartedAt: 2018-10-16 00:23:01 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:30:10 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 429.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flagme.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flagme_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/flagme.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 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  39.948  0.184  40.191
plotSpectra          28.140  0.112  28.273
corPrt               28.044  0.164  28.239
ndpRT                27.612  0.092  27.730
peaksAlignment       27.116  0.116  27.251
dynRT                26.656  0.084  26.761
retFatMatrix         16.160  0.076  16.256
addXCMSPeaks          8.652  0.296   8.976
imputePeaks           8.812  0.012   8.838
plot                  7.836  0.008   7.851
calcTimeDiffs         7.076  0.036   7.164
rmaFitUnit            6.116  0.008   6.136
multipleAlignment     5.956  0.004   5.960
progressiveAlignment  5.656  0.020   5.682
gatherInfo            5.664  0.008   5.673
compress              5.464  0.032   5.501
clusterAlignment      5.276  0.044   5.326
normDotProduct        5.156  0.020   5.180
dp                    5.004  0.008   5.016
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/flagme.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL flagme
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘flagme’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dp.c -o dp.o
dp.c: In function ‘dp’:
dp.c:263:26: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    D[(i+1)+(j+1)*(nr+1)] = cur_min;
                          ^
dp.c:264:28: warning: ‘tb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    phi[(i+1)+(j+1)*(nr+1)] = tb;
                            ^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/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	4.300	0.104	4.483
addChromaTOFPeaks	3.352	0.044	3.400
addXCMSPeaks	8.652	0.296	8.976
betweenAlignment	0	0	0
calcTimeDiffs	7.076	0.036	7.164
clusterAlignment	5.276	0.044	5.326
compress	5.464	0.032	5.501
corPrt	28.044	0.164	28.239
dp	5.004	0.008	5.016
dynRT	26.656	0.084	26.761
gatherInfo	5.664	0.008	5.673
imputePeaks	8.812	0.012	8.838
multipleAlignment	5.956	0.004	5.960
ndpRT	27.612	0.092	27.730
normDotProduct	5.156	0.020	5.180
parseChromaTOF	2.808	0.000	2.821
parseELU	2.104	0.000	2.105
peaksAlignment	27.116	0.116	27.251
peaksDataset	4.904	0.008	4.915
plot	7.836	0.008	7.851
plotImage	3.268	0.004	3.273
plotMultipleSpectra	39.948	0.184	40.191
plotSpectra	28.140	0.112	28.273
progressiveAlignment	5.656	0.020	5.682
retFatMatrix	16.160	0.076	16.256
rmaFitUnit	6.116	0.008	6.136