Kylie A. Bemis
| Snapshot Date: 2023-03-31 14:00:12 -0400 (Fri, 31 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/Cardinal |
| git_branch: devel |
| git_last_commit: 6a786e0 |
| git_last_commit_date: 2022-11-14 15:04:46 -0400 (Mon, 14 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-04-01 11:05:12 -0400 (Sat, 01 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4551 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4312 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4309 |
| 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: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 265/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Cardinal 3.1.0 (landing page) Kylie A. Bemis
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | TIMEOUT | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: Cardinal |
| Version: 3.1.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cardinal.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Cardinal_3.1.0.tar.gz |
| StartedAt: 2023-04-01 00:01:01 -0400 (Sat, 01 Apr 2023) |
| EndedAt: 2023-04-01 00:05:06 -0400 (Sat, 01 Apr 2023) |
| EllapsedTime: 245.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cardinal.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Cardinal_3.1.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/Cardinal.Rcheck'
* using R Under development (unstable) (2023-03-15 r83984 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Cardinal/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Cardinal' version '3.1.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) topFeatures-methods.Rd:73: Escaped LaTeX specials: \&
* 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-3.17-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 nor [v]sprintf. 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
'F:/biocbuild/bbs-3.17-bioc/meat/Cardinal.Rcheck/00check.log'
for details.
Cardinal.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Cardinal
###
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##############################################################################
* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'Cardinal' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DIP.cpp -o DIP.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imzML.cpp -o imzML.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pugixml.cpp -o pugixml.o
pugixml.cpp:2264:23: 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:2258:25: 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:221:25: 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++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c spatial.cpp -o spatial.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -s -static-libgcc -o Cardinal.dll tmp.def DIP.o imzML.o init.o pugixml.o spatial.o utils.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-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 Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 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: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
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, aperm, 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
>
> test_check("Cardinal")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 282 ]
>
> proc.time()
user system elapsed
61.56 2.01 64.31
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| ImageList-class | 0.05 | 0.00 | 0.05 | |
| ImagingExperiment-class | 0.03 | 0.01 | 0.04 | |
| MSImagingExperiment-class | 0.16 | 0.00 | 0.16 | |
| MSImagingInfo-class | 0.28 | 0.02 | 0.30 | |
| MassDataFrame-class | 0 | 0 | 0 | |
| PCA-methods | 0.69 | 0.06 | 0.75 | |
| PLS-methods | 0.87 | 0.00 | 0.87 | |
| PositionDataFrame-class | 0.02 | 0.00 | 0.02 | |
| SparseImagingExperiment-class | 0.03 | 0.00 | 0.03 | |
| XDataFrame-class | 0.01 | 0.00 | 0.01 | |
| aggregate-methods | 1.33 | 0.02 | 1.36 | |
| colocalized-methods | 0.94 | 0.01 | 0.96 | |
| colors-functions | 0.55 | 0.02 | 0.56 | |
| findNeighbors-methods | 0.07 | 0.00 | 0.08 | |
| image-methods | 0.57 | 0.07 | 0.64 | |
| meansTest-methods | 3.51 | 0.07 | 3.57 | |
| mz-methods | 0 | 0 | 0 | |
| mzAlign-methods | 0.42 | 0.00 | 0.43 | |
| mzBin-methods | 0.32 | 0.01 | 0.32 | |
| mzFilter-methods | 0.76 | 0.02 | 0.79 | |
| normalize-methods | 0.27 | 0.01 | 0.28 | |
| peakAlign-methods | 0.51 | 0.00 | 0.51 | |
| peakBin-methods | 0.35 | 0.00 | 0.35 | |
| peakPick-methods | 0.29 | 0.00 | 0.29 | |
| pixelApply-methods | 0.77 | 0.04 | 0.80 | |
| plot-methods | 0.83 | 0.01 | 0.84 | |
| process-methods | 1.8 | 0.0 | 1.8 | |
| reduceBaseline-methods | 0.31 | 0.00 | 0.31 | |
| simulateSpectrum | 0.95 | 0.02 | 0.97 | |
| slice-methods | 0.39 | 0.00 | 0.39 | |
| smoothSignal-methods | 0.35 | 0.00 | 0.35 | |
| spatialDGMM-methods | 1.81 | 0.07 | 1.89 | |
| spatialFastmap-methods | 0.79 | 0.00 | 0.79 | |
| spatialKMeans-methods | 1.36 | 0.05 | 1.41 | |
| spatialShrunkenCentroids-methods | 2.94 | 0.01 | 2.95 | |
| subset-methods | 0.5 | 0.0 | 0.5 | |
| topFeatures-methods | 0.85 | 0.03 | 0.87 | |