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CHECK report for Cardinal on malbec2

This page was generated on 2018-10-17 08:27:11 -0400 (Wed, 17 Oct 2018).

Package 189/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 1.12.1
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)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
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###
### 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
###
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* 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.



Installation output

Cardinal.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output

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 

Example timings

Cardinal.Rcheck/Cardinal-Ex.timings

nameusersystemelapsed
Binmat-class0.0000.0000.001
Hashmat-class0.0880.0160.105
IAnnotatedDataFrame-class0.1000.0000.098
ImageData-class0.0200.0000.019
MIAPE-Imaging-class0.0040.0000.004
MSImageData-class0.0880.0000.085
MSImageProcess-class0.0000.0000.002
MSImageSet-class0.2200.0040.227
OPLS-methods0.0880.0000.088
PCA-methods0.0360.0040.039
PLS-methods0.0680.0000.071
SImageData-class0.040.000.04
SImageSet-class0.0440.0040.047
batchProcess-methods0.7040.0080.712
colors-functions0.7760.0000.777
generateImage0.7760.0040.780
generateSpectrum0.0320.0000.033
iSet-class0.0320.0000.035
image-methods0.5360.0000.535
normalize-methods0.10.00.1
peakAlign-methods0.3120.0000.313
peakFilter-methods0.6400.0000.639
peakPick-methods0.1160.0160.130
pixelApply-methods0.0240.0120.035
pixels-methods0.0920.0040.095
plot-methods0.5720.0000.570
reduceBaseline-methods0.1120.0000.113
reduceDimension-methods0.1160.0000.117
smoothSignal-methods.R0.1120.0000.113
spatialKMeans-methods0.3800.0000.381
spatialShrunkenCentroids-methods1.2760.0041.281
standardizeSamples-methods0.3160.0040.320
topLabels-methods0.6960.0000.694