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 08:39:56 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Cardinal.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Cardinal_1.12.1.tar.gz |
| StartedAt: 2018-10-17 00:55:14 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:59:04 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 230.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Cardinal.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Cardinal_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Cardinal.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/Cardinal/libs/i386/Cardinal.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Cardinal.Rcheck/00check.log' for details.
Cardinal.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Cardinal_1.12.1.tar.gz && rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Cardinal.buildbin-libdir Cardinal_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Cardinal_1.12.1.zip && rm Cardinal_1.12.1.tar.gz Cardinal_1.12.1.zip
###
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install for i386
* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c dynamicAlign.c -o dynamicAlign.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c imzML.cpp -o imzML.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c localMaxima.c -o localMaxima.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pugixml.cpp -o pugixml.o
pugixml.cpp:221:18: warning: 'size_t pugi::impl::{anonymous}::strlength_wide(const wchar_t*)' defined but not used [-Wunused-function]
PUGI__FN size_t strlength_wide(const wchar_t* s)
^
pugixml.cpp:2258:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
^
pugixml.cpp:2264:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c smooth.c -o smooth.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c spatial.c -o spatial.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def dynamicAlign.o fastmap.o imzML.o localMaxima.o pugixml.o smooth.o spatial.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Cardinal'
finding HTML links ... done
Binmat-class html
finding level-2 HTML links ... done
Cardinal-package html
Hashmat-class html
IAnnotatedDataFrame-class html
ImageData-class html
MIAPE-Imaging-class html
MSImageData-class html
MSImageProcess-class html
MSImageSet-class html
OPLS-methods html
PCA-methods html
PLS-methods html
ResultSet-class html
SImageData-class html
SImageSet-class html
batchProcess-methods html
colors-functions html
coord-methods html
coregister-methods html
cvApply-methods html
generateImage html
generateSpectrum html
iSet-class html
image-methods html
imageData-methods html
mz-methods html
normalize-methods html
peakAlign-methods html
peakFilter-methods html
peakPick-methods html
pixelApply-methods html
pixelData-methods html
pixelNames-methods html
pixels-methods html
plot-methods html
processingData-methods html
readMSIData html
reduceBaseline-methods html
reduceDimension-methods html
select-methods html
smoothSignal-methods.R html
spatialKMeans-methods html
spatialShrunkenCentroids-methods html
standardizeSamples-methods html
topLabels-methods html
writeMSIData html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c dynamicAlign.c -o dynamicAlign.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c imzML.cpp -o imzML.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c localMaxima.c -o localMaxima.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pugixml.cpp -o pugixml.o
pugixml.cpp:221:18: warning: 'size_t pugi::impl::{anonymous}::strlength_wide(const wchar_t*)' defined but not used [-Wunused-function]
PUGI__FN size_t strlength_wide(const wchar_t* s)
^
pugixml.cpp:2258:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
^
pugixml.cpp:2264:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c smooth.c -o smooth.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c spatial.c -o spatial.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def dynamicAlign.o fastmap.o imzML.o localMaxima.o pugixml.o smooth.o spatial.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Cardinal' as Cardinal_1.12.1.zip
* DONE (Cardinal)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Cardinal' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
Cardinal.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
28.60 0.37 28.98
|
Cardinal.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
28.59 0.29 28.87
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Cardinal.Rcheck/examples_i386/Cardinal-Ex.timings
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Cardinal.Rcheck/examples_x64/Cardinal-Ex.timings
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