Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-23 11:44 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1160/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
matter 2.9.1 (landing page) Kylie A. Bemis
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the matter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/matter.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. |
Package: matter |
Version: 2.9.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:matter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings matter_2.9.1.tar.gz |
StartedAt: 2024-12-22 21:30:31 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 21:34:26 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 234.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: matter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:matter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings matter_2.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/matter.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘matter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘matter’ version ‘2.9.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘matter’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: SnowfastParam-class.Rd: SnowParam, BiocParallelParam, MulticoreParam checksum.Rd: digest chunkApply.Rd: bplapply colscale.Rd: bplapply cv_do.Rd: bplapply matter-options.Rd: bplapply nscentroids.Rd: bplapply pls.Rd: bplapply prcomp.Rd: bplapply rowDists.Rd: bplapply rowStats.Rd: bplapply sgmix.Rd: bplapply Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 is not available File ‘matter/libs/matter.so’: Found non-API calls to R: ‘R_tryWrap’, ‘STRING_PTR’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/matter.Rcheck/00check.log’ for details.
matter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL matter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘matter’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c altrep.cpp -o altrep.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c init.cpp -o init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c matterExports.cpp -o matterExports.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o matter.so altrep.o init.o matterExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-matter/00new/matter/libs ** R ** 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 (matter)
matter.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(matter) Loading required package: BiocParallel Loading required package: Matrix > > test_check("matter") | | | 0% | |==== | 5% | |======= | 10% | |========== | 15% | |============== | 20% | |================== | 25% | |===================== | 30% | |======================== | 35% | |============================ | 40% | |================================ | 45% | |=================================== | 50% | |====================================== | 55% | |========================================== | 60% | |============================================== | 65% | |================================================= | 70% | |==================================================== | 75% | |======================================================== | 80% | |============================================================ | 85% | |=============================================================== | 90% | |================================================================== | 95% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 7 | PASS 2044 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • empty test (7): 'test-vizi.R:256:1', 'test-vizi.R:296:1', 'test-vizi.R:316:1', 'test-vizi.R:337:1', 'test-vizi.R:364:1', 'test-vizi.R:424:1', 'test-vizi.R:467:1' [ FAIL 0 | WARN 0 | SKIP 7 | PASS 2044 ] > > proc.time() user system elapsed 87.693 5.036 113.687
matter.Rcheck/matter-Ex.timings
name | user | system | elapsed | |
RNGStreams | 0.918 | 0.009 | 0.933 | |
SnowfastParam-class | 0.205 | 0.025 | 2.815 | |
approx1 | 0.002 | 0.001 | 0.004 | |
approx2 | 0.004 | 0.000 | 0.005 | |
avg | 0.002 | 0.000 | 0.001 | |
binpeaks | 0.005 | 0.001 | 0.006 | |
binvec | 0.000 | 0.001 | 0.000 | |
bsearch | 0.000 | 0.000 | 0.001 | |
checksum | 0.027 | 0.005 | 0.035 | |
chunkApply | 0.214 | 0.018 | 0.234 | |
chunked-class | 0.008 | 0.002 | 0.010 | |
colscale | 0.183 | 0.004 | 0.188 | |
colsweep | 0.024 | 0.000 | 0.025 | |
convolve_at | 0.092 | 0.005 | 0.098 | |
coscore | 0.045 | 0.007 | 0.051 | |
cpal | 0.003 | 0.000 | 0.003 | |
cv_do | 0.173 | 0.003 | 0.177 | |
deferred-ops | 0.240 | 0.012 | 0.255 | |
downsample | 0.037 | 0.002 | 0.038 | |
drle-class | 0.001 | 0.000 | 0.002 | |
enhance | 0.025 | 0.002 | 0.029 | |
estbase | 0.011 | 0.002 | 0.013 | |
estdim | 0.003 | 0.000 | 0.004 | |
estnoise | 0.035 | 0.004 | 0.040 | |
estres | 0.002 | 0.000 | 0.001 | |
fastmap | 0.143 | 0.002 | 0.146 | |
fetch | 0.125 | 0.012 | 0.137 | |
filt1 | 0.033 | 0.004 | 0.038 | |
filt2 | 0.026 | 0.001 | 0.028 | |
filtn | 0.003 | 0.001 | 0.004 | |
findpeaks | 0.023 | 0.004 | 0.029 | |
findpeaks_cwt | 0.130 | 0.015 | 0.149 | |
findpeaks_knn | 0.003 | 0.001 | 0.003 | |
iQuote | 0.001 | 0.000 | 0.000 | |
inpoly | 0.004 | 0.000 | 0.004 | |
isofun | 0.026 | 0.001 | 0.027 | |
knnsearch | 0.002 | 0.000 | 0.002 | |
matter-class | 0.030 | 0.003 | 0.034 | |
matter_arr-class | 0.030 | 0.002 | 0.032 | |
matter_fct-class | 0.021 | 0.002 | 0.022 | |
matter_list-class | 0.009 | 0.002 | 0.011 | |
matter_str-class | 0.026 | 0.003 | 0.030 | |
mem | 0.462 | 0.007 | 0.474 | |
mi_learn | 0.645 | 0.009 | 0.658 | |
nnmf | 0.048 | 0.001 | 0.048 | |
nscentroids | 0.117 | 0.001 | 0.119 | |
peakwidths | 0.001 | 0.000 | 0.001 | |
pinv | 0.001 | 0.001 | 0.003 | |
plot_signal | 0.465 | 0.049 | 0.518 | |
pls | 0.040 | 0.000 | 0.041 | |
prcomp | 0.111 | 0.016 | 0.127 | |
predscore | 0.001 | 0.000 | 0.001 | |
rescale | 0.001 | 0.000 | 0.001 | |
rocscore | 0.003 | 0.000 | 0.004 | |
rollvec | 0.001 | 0.000 | 0.001 | |
rowDists | 0.107 | 0.004 | 0.111 | |
rowStats | 0.119 | 0.006 | 0.126 | |
seq_rel | 0.001 | 0.001 | 0.002 | |
sgmix | 2.564 | 0.051 | 2.627 | |
shingles | 0.002 | 0.001 | 0.003 | |
simple_logger-class | 0.004 | 0.002 | 0.006 | |
simspec | 0.032 | 0.004 | 0.036 | |
sparse_arr-class | 0.008 | 0.001 | 0.009 | |
stream_stat | 0.006 | 0.001 | 0.007 | |
struct | 0.006 | 0.002 | 0.007 | |
summary-stats | 0.354 | 0.015 | 0.371 | |
to_raster | 0.003 | 0.001 | 0.005 | |
trans2d | 0.039 | 0.001 | 0.041 | |
uuid | 0.001 | 0.000 | 0.002 | |
vizi-functions | 0.055 | 0.006 | 0.063 | |
warp1 | 0.025 | 0.003 | 0.029 | |
warp2 | 0.891 | 0.010 | 0.906 | |