Mark Robinson
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/flagme |
| Branch: RELEASE_3_6 |
| Last Commit: a5ee896 |
| Last Changed Date: 2017-10-30 12:39:24 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:08:33 -0400 (Thu, 12 Apr 2018).
| Package 467/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flagme 1.34.0 Mark Robinson
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: flagme |
| Version: 1.34.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flagme_1.34.0.tar.gz |
| StartedAt: 2018-04-11 23:26:43 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:34:51 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 488.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flagme.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flagme_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/flagme.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.34.0’
* 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 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 ... 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 ... 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 42.232 0.252 42.586
plotSpectra 30.596 0.136 30.758
ndpRT 30.104 0.092 30.230
dynRT 29.808 0.140 29.970
corPrt 29.560 0.192 29.831
peaksAlignment 29.272 0.132 29.436
retFatMatrix 16.404 0.080 16.496
imputePeaks 10.272 0.012 10.302
plot 8.776 0.024 8.808
rmaFitUnit 8.388 0.008 8.402
addXCMSPeaks 7.948 0.152 8.122
multipleAlignment 7.304 0.004 7.317
calcTimeDiffs 6.992 0.036 7.127
progressiveAlignment 6.540 0.012 6.562
gatherInfo 6.396 0.012 6.413
clusterAlignment 6.292 0.024 6.318
peaksDataset 6.160 0.008 6.178
compress 5.920 0.032 5.958
addAMDISPeaks 5.832 0.056 6.125
normDotProduct 5.664 0.012 5.682
dp 5.284 0.032 5.319
* 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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/flagme.Rcheck/00check.log’
for details.
flagme.Rcheck/00install.out
* installing *source* package ‘flagme’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pearson.c -o pearson.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/flagme.Rcheck/flagme/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flagme)
flagme.Rcheck/flagme-Ex.timings
| name | user | system | elapsed | |
| addAMDISPeaks | 5.832 | 0.056 | 6.125 | |
| addChromaTOFPeaks | 3.292 | 0.052 | 3.345 | |
| addXCMSPeaks | 7.948 | 0.152 | 8.122 | |
| betweenAlignment | 0 | 0 | 0 | |
| calcTimeDiffs | 6.992 | 0.036 | 7.127 | |
| clusterAlignment | 6.292 | 0.024 | 6.318 | |
| compress | 5.920 | 0.032 | 5.958 | |
| corPrt | 29.560 | 0.192 | 29.831 | |
| dp | 5.284 | 0.032 | 5.319 | |
| dynRT | 29.808 | 0.140 | 29.970 | |
| gatherInfo | 6.396 | 0.012 | 6.413 | |
| imputePeaks | 10.272 | 0.012 | 10.302 | |
| multipleAlignment | 7.304 | 0.004 | 7.317 | |
| ndpRT | 30.104 | 0.092 | 30.230 | |
| normDotProduct | 5.664 | 0.012 | 5.682 | |
| parseChromaTOF | 2.688 | 0.000 | 2.707 | |
| parseELU | 2.376 | 0.008 | 2.383 | |
| peaksAlignment | 29.272 | 0.132 | 29.436 | |
| peaksDataset | 6.160 | 0.008 | 6.178 | |
| plot | 8.776 | 0.024 | 8.808 | |
| plotImage | 2.996 | 0.004 | 2.999 | |
| plotMultipleSpectra | 42.232 | 0.252 | 42.586 | |
| plotSpectra | 30.596 | 0.136 | 30.758 | |
| progressiveAlignment | 6.540 | 0.012 | 6.562 | |
| retFatMatrix | 16.404 | 0.080 | 16.496 | |
| rmaFitUnit | 8.388 | 0.008 | 8.402 | |