| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:37 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
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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 250/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Cardinal 3.1.0 (landing page) Kylie A. Bemis
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: Cardinal |
| Version: 3.1.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Cardinal_3.1.0.tar.gz |
| StartedAt: 2023-02-27 22:36:43 -0000 (Mon, 27 Feb 2023) |
| EndedAt: 2023-02-27 22:44:43 -0000 (Mon, 27 Feb 2023) |
| EllapsedTime: 480.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Cardinal.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Cardinal_3.1.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Cardinal.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Cardinal’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/library/Cardinal/libs/Cardinal.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (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 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 ...
‘Cardinal-3-guide.Rmd’ using ‘UTF-8’... OK
‘Cardinal-3-stats.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/Cardinal.Rcheck/00check.log’
for details.
Cardinal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Cardinal ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘Cardinal’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c DIP.cpp -o DIP.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c imzML.cpp -o imzML.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init.cpp -o init.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c pugixml.cpp -o pugixml.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c spatial.cpp -o spatial.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o Cardinal.so DIP.o imzML.o init.o pugixml.o spatial.o utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-Cardinal/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** 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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
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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
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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 396 | SKIP 0 | PASS 282 ]
[ FAIL 0 | WARN 396 | SKIP 0 | PASS 282 ]
>
> proc.time()
user system elapsed
73.687 1.892 75.749
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| ImageList-class | 0.059 | 0.008 | 0.067 | |
| ImagingExperiment-class | 0.048 | 0.000 | 0.048 | |
| MSImagingExperiment-class | 0.129 | 0.004 | 0.133 | |
| MSImagingInfo-class | 0.291 | 0.032 | 0.323 | |
| MassDataFrame-class | 0.009 | 0.000 | 0.009 | |
| PCA-methods | 0.821 | 0.056 | 0.877 | |
| PLS-methods | 1.362 | 0.020 | 1.383 | |
| PositionDataFrame-class | 0.018 | 0.003 | 0.021 | |
| SparseImagingExperiment-class | 0.035 | 0.012 | 0.046 | |
| XDataFrame-class | 0.012 | 0.000 | 0.013 | |
| aggregate-methods | 1.622 | 0.044 | 1.667 | |
| colocalized-methods | 1.176 | 0.028 | 1.205 | |
| colors-functions | 1.036 | 0.020 | 1.056 | |
| findNeighbors-methods | 0.057 | 0.016 | 0.073 | |
| image-methods | 0.903 | 0.012 | 0.915 | |
| meansTest-methods | 4.141 | 0.132 | 4.274 | |
| mz-methods | 0.002 | 0.000 | 0.002 | |
| mzAlign-methods | 0.597 | 0.004 | 0.601 | |
| mzBin-methods | 0.387 | 0.000 | 0.387 | |
| mzFilter-methods | 1.12 | 0.00 | 1.12 | |
| normalize-methods | 0.374 | 0.028 | 0.402 | |
| peakAlign-methods | 0.711 | 0.016 | 0.727 | |
| peakBin-methods | 0.423 | 0.004 | 0.427 | |
| peakPick-methods | 0.438 | 0.000 | 0.438 | |
| pixelApply-methods | 1.022 | 0.020 | 1.042 | |
| plot-methods | 1.167 | 0.064 | 1.231 | |
| process-methods | 1.584 | 0.048 | 1.632 | |
| reduceBaseline-methods | 0.456 | 0.000 | 0.456 | |
| simulateSpectrum | 1.016 | 0.008 | 1.024 | |
| slice-methods | 0.480 | 0.004 | 0.485 | |
| smoothSignal-methods | 0.432 | 0.004 | 0.435 | |
| spatialDGMM-methods | 2.194 | 0.012 | 2.206 | |
| spatialFastmap-methods | 0.721 | 0.000 | 0.721 | |
| spatialKMeans-methods | 1.788 | 0.028 | 1.815 | |
| spatialShrunkenCentroids-methods | 3.593 | 0.032 | 3.625 | |
| subset-methods | 0.602 | 0.007 | 0.610 | |
| topFeatures-methods | 1.059 | 0.005 | 1.062 | |