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This page was generated on 2024-03-28 11:37:26 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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

Package 271/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 3.5.0  (landing page)
Kylie A. Bemis
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/Cardinal
git_branch: devel
git_last_commit: b0496ea
git_last_commit_date: 2023-11-22 14:25:11 -0400 (Wed, 22 Nov 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Cardinal on palomino3


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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Cardinal
Version: 3.5.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cardinal.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Cardinal_3.5.0.tar.gz
StartedAt: 2024-03-28 00:07:12 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 00:11:23 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 250.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Cardinal.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cardinal.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Cardinal_3.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/Cardinal.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '3.5.0'
* 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) 13.2.0'
* 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 code 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 whether 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) pixelApply-methods.Rd:72: Lost braces
    72 |     For \code{pixelApply}, the function is applied to the feature vector belonging to each pixel. The use of \code{.feature.groups} allows code{\link{tapply}}-like functionality on the feature vectors, applied separately to each pixel.
       |                                                                                                                                                ^
checkRd: (-1) pixelApply-methods.Rd:74: Lost braces
    74 |     For \code{featureApply}, the function is applied to the vector of intensity values (i.e., the flattened image) corresponding to each feature. The use of \code{.feature.groups} allows code{\link{tapply}}-like functionality on the flattened image intensity vectors, applied separately to each feature.
       |                                                                                                                                                                                                ^
* 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-3.19-bioc/R/library/Cardinal/libs/x64/Cardinal.dll':
  Found '_exit', possibly from '_exit' (C)
  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 ... 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-3.19-bioc/meat/Cardinal.Rcheck/00check.log'
for details.


Installation output

Cardinal.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Cardinal
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'Cardinal' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-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)

Tests output

Cardinal.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, 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 object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

> 
> test_check("Cardinal")
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 284 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 284 ]
> 
> proc.time()
   user  system elapsed 
  62.67    3.26   66.78 

Example timings

Cardinal.Rcheck/Cardinal-Ex.timings

nameusersystemelapsed
ImageList-class0.110.000.10
ImagingExperiment-class0.040.000.05
MSImagingExperiment-class0.140.010.16
MSImagingInfo-class0.330.020.34
MassDataFrame-class0.010.000.02
PCA-methods0.890.010.91
PLS-methods0.610.030.64
PositionDataFrame-class0.020.000.01
SparseImagingExperiment-class0.030.000.03
XDataFrame-class0.020.000.02
aggregate-methods1.180.041.22
colocalized-methods1.000.041.04
colors-functions0.660.030.69
findNeighbors-methods0.090.000.09
image-methods1.190.021.22
meansTest-methods2.670.122.80
mz-methods000
mzAlign-methods0.370.020.39
mzBin-methods0.280.020.29
mzFilter-methods0.710.000.71
normalize-methods0.360.000.36
peakAlign-methods0.610.000.61
peakBin-methods0.260.000.27
peakPick-methods0.250.020.26
pixelApply-methods0.360.030.39
plot-methods0.750.030.79
process-methods1.190.031.21
reduceBaseline-methods0.30.00.3
simulateSpectrum0.670.020.70
slice-methods0.390.010.41
smoothSignal-methods0.280.000.28
spatialDGMM-methods1.520.081.60
spatialFastmap-methods0.580.030.61
spatialKMeans-methods1.310.001.31
spatialShrunkenCentroids-methods2.560.032.60
subset-methods0.430.030.45
topFeatures-methods0.730.020.75