Kylie A. Bemis
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/Cardinal |
| Branch: RELEASE_3_7 |
| Last Commit: 8885df8 |
| Last Changed Date: 2018-07-22 17:06:58 -0400 (Sun, 22 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:27:11 -0400 (Wed, 17 Oct 2018).
| Package 189/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Cardinal 1.12.1 Kylie A. Bemis
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Cardinal |
| Version: 1.12.1 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Cardinal_1.12.1.tar.gz |
| StartedAt: 2018-10-15 22:59:58 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:01:49 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 110.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Cardinal_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/Cardinal.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 ‘Cardinal/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Cardinal’ version ‘1.12.1’ * 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 ‘Cardinal’ can be installed ... 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 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 ... NOTE batchProcess,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ normalize,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ peakAlign,MSImageSet-numeric : <anonymous>: no visible binding for global variable ‘.Index’ peakPick,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ reduceBaseline,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ reduceDimension,MSImageSet-missing : <anonymous>: no visible binding for global variable ‘.Index’ smoothSignal,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ Undefined global functions or variables: .Index * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/Cardinal.Rcheck/00check.log’ for details.
Cardinal.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL Cardinal
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘Cardinal’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dynamicAlign.c -o dynamicAlign.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastmap.c -o fastmap.o
fastmap.c: In function ‘choose_distant_objects’:
fastmap.c:59:24: warning: ‘o_b’ may be used uninitialized in this function [-Wmaybe-uninitialized]
pivot_objects->b[col] = o_b;
^
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c imzML.cpp -o imzML.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c localMaxima.c -o localMaxima.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pugixml.cpp -o pugixml.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c smooth.c -o smooth.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c spatial.c -o spatial.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o Cardinal.so dynamicAlign.o fastmap.o imzML.o localMaxima.o pugixml.o smooth.o spatial.o utils.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/Cardinal/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Cardinal)
Cardinal.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Cardinal)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: matter
Loading required package: biglm
Loading required package: DBI
Attaching package: 'matter'
The following object is masked from 'package:biglm':
biglm
The following objects are masked from 'package:base':
apply, scale
Loading required package: ProtGenerics
Welcome to Cardinal (version 1.12.1)
To get started, view the introductory vignettes with
'browseVignettes("Cardinal")'.
>
> test_check("Cardinal")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 229 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
23.356 0.220 23.636
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| Binmat-class | 0.000 | 0.000 | 0.001 | |
| Hashmat-class | 0.088 | 0.016 | 0.105 | |
| IAnnotatedDataFrame-class | 0.100 | 0.000 | 0.098 | |
| ImageData-class | 0.020 | 0.000 | 0.019 | |
| MIAPE-Imaging-class | 0.004 | 0.000 | 0.004 | |
| MSImageData-class | 0.088 | 0.000 | 0.085 | |
| MSImageProcess-class | 0.000 | 0.000 | 0.002 | |
| MSImageSet-class | 0.220 | 0.004 | 0.227 | |
| OPLS-methods | 0.088 | 0.000 | 0.088 | |
| PCA-methods | 0.036 | 0.004 | 0.039 | |
| PLS-methods | 0.068 | 0.000 | 0.071 | |
| SImageData-class | 0.04 | 0.00 | 0.04 | |
| SImageSet-class | 0.044 | 0.004 | 0.047 | |
| batchProcess-methods | 0.704 | 0.008 | 0.712 | |
| colors-functions | 0.776 | 0.000 | 0.777 | |
| generateImage | 0.776 | 0.004 | 0.780 | |
| generateSpectrum | 0.032 | 0.000 | 0.033 | |
| iSet-class | 0.032 | 0.000 | 0.035 | |
| image-methods | 0.536 | 0.000 | 0.535 | |
| normalize-methods | 0.1 | 0.0 | 0.1 | |
| peakAlign-methods | 0.312 | 0.000 | 0.313 | |
| peakFilter-methods | 0.640 | 0.000 | 0.639 | |
| peakPick-methods | 0.116 | 0.016 | 0.130 | |
| pixelApply-methods | 0.024 | 0.012 | 0.035 | |
| pixels-methods | 0.092 | 0.004 | 0.095 | |
| plot-methods | 0.572 | 0.000 | 0.570 | |
| reduceBaseline-methods | 0.112 | 0.000 | 0.113 | |
| reduceDimension-methods | 0.116 | 0.000 | 0.117 | |
| smoothSignal-methods.R | 0.112 | 0.000 | 0.113 | |
| spatialKMeans-methods | 0.380 | 0.000 | 0.381 | |
| spatialShrunkenCentroids-methods | 1.276 | 0.004 | 1.281 | |
| standardizeSamples-methods | 0.316 | 0.004 | 0.320 | |
| topLabels-methods | 0.696 | 0.000 | 0.694 | |