Kylie A. Bemis
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/Cardinal |
| git_branch: master |
| git_last_commit: 4bd3fdf |
| git_last_commit_date: 2021-11-21 05:19:35 -0400 (Sun, 21 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:06 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the Cardinal package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Cardinal.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 244/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Cardinal 2.13.1 (landing page) Kylie A. Bemis
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Cardinal |
| Version: 2.13.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cardinal.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Cardinal_2.13.1.tar.gz |
| StartedAt: 2022-03-17 18:38:36 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:42:39 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 243.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cardinal.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Cardinal_2.13.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Cardinal.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '2.13.1'
* 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 ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
R 2.8Mb
help 1.7Mb
* 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 ... OK
* 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/Cardinal/libs/x64/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 ... 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
'D:/biocbuild/bbs-3.15-bioc/meat/Cardinal.Rcheck/00check.log'
for details.
Cardinal.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Cardinal
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Cardinal' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c DIP.cpp -o DIP.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c dynAlign.cpp -o dynAlign.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c imzML.cpp -o imzML.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c init.cpp -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pugixml.cpp -o pugixml.o
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)
^~~~~~~~~~~
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: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)
^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c spatial.cpp -o spatial.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Cardinal.dll tmp.def DIP.o dynAlign.o imzML.o init.o pugixml.o spatial.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Cardinal/00new/Cardinal/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Cardinal'
finding HTML links ... done
AnnotatedImage-class html
finding level-2 HTML links ... done
AnnotatedImagingExperiment-class html
Cardinal-package html
ImageList-class html
ImagingExperiment-class html
ImagingResult-class html
MSContinuousImagingExperiment-class html
MSImagingExperiment-class html
MSImagingInfo-class html
MSProcessedImagingExperiment-class html
MassDataFrame-class html
PCA-methods html
PLS-methods html
PositionDataFrame-class html
SparseImagingExperiment-class html
XDataFrame-class html
aggregate-methods html
colocalized-methods html
colors-functions html
crossValidate-methods html
defunct html
deprecated html
findNeighbors-methods html
image-methods html
internal html
legacy html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Cardinal/00new/Cardinal/help/ImageData.html
meansTest-methods html
mz-methods html
mzAlign-methods html
mzBin-methods html
mzFilter-methods html
normalize-methods html
peakAlign-methods html
peakBin-methods html
peakPick-methods html
pixelApply-methods html
plot-methods html
process-methods html
readMSIData html
reduceBaseline-methods html
reexports html
selectROI-methods html
simulateSpectrum html
slice-methods html
smoothSignal-methods html
spatialDGMM-methods html
spatialFastmap-methods html
spatialKMeans-methods html
spatialShrunkenCentroids-methods html
subset-methods html
topFeatures-methods html
writeMSIData html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Cardinal)
Making 'packages.html' ... done
Cardinal.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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
Attaching package: 'BiocGenerics'
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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: BiocParallel
Loading required package: EBImage
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
Attaching package: 'Cardinal'
The following object is masked from 'package:stats':
filter
>
> test_check("Cardinal")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 304 ]
>
> proc.time()
user system elapsed
61.26 0.96 63.37
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| AnnotatedImagingExperiment-class | 0 | 0 | 0 | |
| ImageList-class | 0.07 | 0.00 | 0.06 | |
| ImagingExperiment-class | 0.03 | 0.00 | 0.03 | |
| MSImagingExperiment-class | 0.06 | 0.04 | 0.10 | |
| MSImagingInfo-class | 0.22 | 0.00 | 0.21 | |
| MassDataFrame-class | 0 | 0 | 0 | |
| PCA-methods | 0.50 | 0.01 | 0.52 | |
| PLS-methods | 0.55 | 0.00 | 0.55 | |
| PositionDataFrame-class | 0.01 | 0.00 | 0.01 | |
| SparseImagingExperiment-class | 0.02 | 0.00 | 0.02 | |
| XDataFrame-class | 0.01 | 0.00 | 0.01 | |
| aggregate-methods | 1.21 | 0.00 | 1.21 | |
| colocalized-methods | 0.79 | 0.00 | 0.79 | |
| colors-functions | 0.44 | 0.00 | 0.44 | |
| findNeighbors-methods | 0.05 | 0.02 | 0.06 | |
| image-methods | 0.62 | 0.00 | 0.63 | |
| meansTest-methods | 2.53 | 0.17 | 2.70 | |
| mz-methods | 0 | 0 | 0 | |
| mzAlign-methods | 0.59 | 0.00 | 0.59 | |
| mzBin-methods | 0.35 | 0.00 | 0.35 | |
| mzFilter-methods | 1.01 | 0.00 | 1.01 | |
| normalize-methods | 0.35 | 0.00 | 0.34 | |
| peakAlign-methods | 0.64 | 0.00 | 0.65 | |
| peakBin-methods | 0.36 | 0.00 | 0.35 | |
| peakPick-methods | 0.36 | 0.00 | 0.36 | |
| pixelApply-methods | 0.92 | 0.00 | 0.93 | |
| plot-methods | 0.97 | 0.03 | 1.00 | |
| process-methods | 1.06 | 0.05 | 1.11 | |
| reduceBaseline-methods | 0.4 | 0.0 | 0.4 | |
| simulateSpectrum | 0.99 | 0.01 | 1.00 | |
| slice-methods | 0.3 | 0.0 | 0.3 | |
| smoothSignal-methods | 0.32 | 0.00 | 0.36 | |
| spatialDGMM-methods | 2.16 | 0.02 | 2.25 | |
| spatialFastmap-methods | 0.95 | 0.00 | 0.95 | |
| spatialKMeans-methods | 2.43 | 0.00 | 2.44 | |
| spatialShrunkenCentroids-methods | 3.59 | 0.00 | 3.59 | |
| subset-methods | 0.34 | 0.00 | 0.35 | |
| topFeatures-methods | 1.27 | 0.00 | 1.26 | |