Kylie A. Bemis
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/Cardinal |
| git_branch: RELEASE_3_15 |
| git_last_commit: 1c8f02e |
| git_last_commit_date: 2022-04-26 11:23:41 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:21:13 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 252/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Cardinal 2.14.0 (landing page) Kylie A. Bemis
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | 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: 2.14.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cardinal.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Cardinal_2.14.0.tar.gz |
| StartedAt: 2022-10-18 22:39:47 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 22:44:49 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 302.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cardinal.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Cardinal_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/Cardinal.Rcheck' * using R version 4.2.1 (2022-06-23 ucrt) * using platform: x86_64-w64-mingw32 (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 '2.14.0' * 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 * 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 'F:/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) 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: 1 NOTE See 'F:/biocbuild/bbs-3.15-bioc/meat/Cardinal.Rcheck/00check.log' for details.
Cardinal.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Cardinal
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Cardinal' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DIP.cpp -o DIP.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dynAlign.cpp -o dynAlign.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imzML.cpp -o imzML.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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]
2264 | 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]
2258 | 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]
221 | PUGI__FN size_t strlength_wide(const wchar_t* s)
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c spatial.cpp -o spatial.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/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
** 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)
Cardinal.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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
91.71 2.32 94.65
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| AnnotatedImagingExperiment-class | 0 | 0 | 0 | |
| ImageList-class | 0.11 | 0.01 | 0.13 | |
| ImagingExperiment-class | 0.06 | 0.00 | 0.07 | |
| MSImagingExperiment-class | 0.09 | 0.00 | 0.09 | |
| MSImagingInfo-class | 0.21 | 0.02 | 0.22 | |
| MassDataFrame-class | 0 | 0 | 0 | |
| PCA-methods | 0.62 | 0.01 | 0.64 | |
| PLS-methods | 0.81 | 0.00 | 0.81 | |
| PositionDataFrame-class | 0.02 | 0.00 | 0.01 | |
| SparseImagingExperiment-class | 0.05 | 0.00 | 0.05 | |
| XDataFrame-class | 0.01 | 0.00 | 0.02 | |
| aggregate-methods | 1.67 | 0.02 | 1.68 | |
| colocalized-methods | 1.6 | 0.0 | 1.6 | |
| colors-functions | 0.62 | 0.00 | 0.62 | |
| findNeighbors-methods | 0.06 | 0.03 | 0.10 | |
| image-methods | 0.94 | 0.00 | 0.93 | |
| meansTest-methods | 2.95 | 0.09 | 3.05 | |
| mz-methods | 0 | 0 | 0 | |
| mzAlign-methods | 0.44 | 0.00 | 0.44 | |
| mzBin-methods | 0.3 | 0.0 | 0.3 | |
| mzFilter-methods | 1.11 | 0.02 | 1.12 | |
| normalize-methods | 0.76 | 0.00 | 0.77 | |
| peakAlign-methods | 0.7 | 0.0 | 0.7 | |
| peakBin-methods | 0.3 | 0.0 | 0.3 | |
| peakPick-methods | 0.47 | 0.00 | 0.47 | |
| pixelApply-methods | 0.64 | 0.00 | 0.64 | |
| plot-methods | 0.81 | 0.01 | 0.83 | |
| process-methods | 1.02 | 0.02 | 1.03 | |
| reduceBaseline-methods | 0.45 | 0.00 | 0.45 | |
| simulateSpectrum | 0.53 | 0.02 | 0.55 | |
| slice-methods | 0.56 | 0.01 | 0.58 | |
| smoothSignal-methods | 0.47 | 0.00 | 0.47 | |
| spatialDGMM-methods | 1.56 | 0.06 | 1.63 | |
| spatialFastmap-methods | 0.78 | 0.00 | 0.78 | |
| spatialKMeans-methods | 2.89 | 0.04 | 2.92 | |
| spatialShrunkenCentroids-methods | 4.24 | 0.06 | 4.30 | |
| subset-methods | 0.59 | 0.00 | 0.59 | |
| topFeatures-methods | 1.86 | 0.06 | 1.92 | |