Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:39 -0500 (Tue, 24 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" | 4373 |
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 41/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
alabaster.base 1.7.2 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the alabaster.base package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.base.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: alabaster.base |
Version: 1.7.2 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings alabaster.base_1.7.2.tar.gz |
StartedAt: 2024-12-23 19:39:50 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 19:41:36 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 106.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: alabaster.base.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings alabaster.base_1.7.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.base.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘alabaster.base/DESCRIPTION’ ... OK * this is package ‘alabaster.base’ version ‘1.7.2’ * package encoding: UTF-8 * 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 ‘alabaster.base’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... OK * checking installed package size ... INFO installed size is 18.0Mb sub-directories of 1Mb or more: libs 17.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Versioned 'LinkingTo' value for ‘assorthead’ is only usable in R >= 3.0.2 * 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 loading without being on the library search path ... 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 ... 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... INFO GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/alabaster.base/libs/alabaster.base.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘abort’, possibly from ‘abort’ (C) Found ‘exit’, possibly from ‘exit’ (C) Found ‘rand_r’, possibly from ‘rand_r’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.base.Rcheck/00check.log’ for details.
alabaster.base.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL alabaster.base ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘alabaster.base’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c check_csv.cpp -o check_csv.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c check_list.cpp -o check_list.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c is_rfc3339.cpp -o is_rfc3339.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c load_csv.cpp -o load_csv.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c load_list.cpp -o load_list.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c validate.cpp -o validate.o In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/chihaya/validate.hpp:13, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/chihaya/chihaya.hpp:10, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/takane/utils_public.hpp:13, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/takane/_validate.hpp:9, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/takane/takane.hpp:4, from validate.cpp:2: /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = long unsigned int]’: /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here 45 | Index_ previous; | ^~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = int]’: /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here 45 | Index_ previous; | ^~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-alabaster.base/00new/alabaster.base/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 (alabaster.base)
alabaster.base.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(alabaster.base) > test_check("alabaster.base") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 565 ] > > proc.time() user system elapsed 59.384 1.501 48.538
alabaster.base.Rcheck/alabaster.base-Ex.timings
name | user | system | elapsed | |
Rfc3339 | 0.002 | 0.002 | 0.004 | |
acquireFile | 0.630 | 0.032 | 0.588 | |
altReadObject | 0.062 | 0.022 | 0.086 | |
altSaveObject | 0.047 | 0.008 | 0.056 | |
anyMissing | 0 | 0 | 0 | |
chooseMissingPlaceholderForHdf5 | 0.000 | 0.001 | 0.001 | |
createRedirection | 0.379 | 0.019 | 0.332 | |
listObjects | 0.074 | 0.004 | 0.078 | |
loadDirectory | 0.701 | 0.019 | 0.561 | |
moveObject | 0.730 | 0.046 | 0.638 | |
quickLoadObject | 0.754 | 0.058 | 0.564 | |
quickReadCsv | 0.041 | 0.003 | 0.043 | |
readAtomicVector | 0.016 | 0.004 | 0.021 | |
readBaseFactor | 0.015 | 0.002 | 0.017 | |
readBaseList | 0.082 | 0.008 | 0.090 | |
readDataFrame | 0.067 | 0.003 | 0.070 | |
readDataFrameFactor | 0.196 | 0.009 | 0.204 | |
readObject | 0.062 | 0.002 | 0.064 | |
readObjectFile | 0.001 | 0.001 | 0.001 | |
removeObject | 0.686 | 0.008 | 0.526 | |
saveAtomicVector | 0.019 | 0.000 | 0.019 | |
saveBaseFactor | 0.008 | 0.002 | 0.009 | |
saveBaseList | 0.048 | 0.001 | 0.049 | |
saveDataFrameFactor | 0.097 | 0.004 | 0.101 | |
saveFormats | 0 | 0 | 0 | |
saveObject | 0.051 | 0.001 | 0.052 | |
stageDataFrame | 0.046 | 0.002 | 0.048 | |
transformVectorForHdf5 | 0.001 | 0.000 | 0.001 | |
validateDirectory | 0.084 | 0.018 | 0.102 | |
validateObject | 0.046 | 0.008 | 0.053 | |
writeMetadata | 0.301 | 0.017 | 0.246 | |