Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:42 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 695/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FEAST 1.13.0 (landing page) Kenong Su
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the FEAST package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FEAST.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: FEAST |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FEAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FEAST_1.13.0.tar.gz |
StartedAt: 2024-08-15 21:44:09 -0400 (Thu, 15 Aug 2024) |
EndedAt: 2024-08-15 21:52:33 -0400 (Thu, 15 Aug 2024) |
EllapsedTime: 503.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FEAST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FEAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FEAST_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FEAST.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FEAST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FEAST’ version ‘1.13.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES' 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 ‘FEAST’ 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 ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: data 3.9Mb doc 1.5Mb * 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 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 ... NOTE FEAST: multiple local function definitions for ‘bp_fun’ with different formal arguments SC3_Clust: no visible global function definition for ‘metadata’ Visual_Rslt: no visible global function definition for ‘ggbarplot’ Visual_Rslt: no visible global function definition for ‘theme’ Visual_Rslt: no visible global function definition for ‘element_text’ Visual_Rslt: no visible global function definition for ‘ggline’ Visual_Rslt: no visible global function definition for ‘get_palette’ Visual_Rslt: no visible global function definition for ‘scale_y_continuous’ Visual_Rslt: no visible global function definition for ‘guides’ Visual_Rslt: no visible global function definition for ‘guide_legend’ Visual_Rslt: no visible global function definition for ‘ggarrange’ aricode_NMI : entropy: no visible global function definition for ‘sortPairs’ Undefined global functions or variables: element_text get_palette ggarrange ggbarplot ggline guide_legend guides metadata scale_y_continuous sortPairs theme * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/FEAST.Rcheck/00check.log’ for details.
FEAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FEAST ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘FEAST’ ... ** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cal_3_metrics.c -o cal_3_metrics.o cal_3_metrics.c:42:38: warning: variable 'nij_2' set but not used [-Wunused-but-set-variable] double *nc, *nr, ni_2, n_j2, nt, nij_2; ^ cal_3_metrics.c:42:22: warning: variable 'ni_2' set but not used [-Wunused-but-set-variable] double *nc, *nr, ni_2, n_j2, nt, nij_2; ^ cal_3_metrics.c:42:28: warning: variable 'n_j2' set but not used [-Wunused-but-set-variable] double *nc, *nr, ni_2, n_j2, nt, nij_2; ^ cal_3_metrics.c:42:34: warning: variable 'nt' set but not used [-Wunused-but-set-variable] double *nc, *nr, ni_2, n_j2, nt, nij_2; ^ 4 warnings generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FEAST.so cal_3_metrics.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-FEAST/00new/FEAST/libs ** R ** data *** moving datasets to lazyload DB ** 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 (FEAST)
FEAST.Rcheck/FEAST-Ex.timings
name | user | system | elapsed | |
Consensus | 1.319 | 0.026 | 1.346 | |
FEAST | 0.749 | 0.008 | 0.759 | |
FEAST_fast | 1.575 | 0.025 | 1.601 | |
Norm_Y | 0.135 | 0.016 | 0.151 | |
Select_Model_short_SC3 | 0.764 | 0.012 | 0.777 | |
Select_Model_short_TSCAN | 0.751 | 0.008 | 0.759 | |
TSCAN_Clust | 0.001 | 0.001 | 0.002 | |
Visual_Rslt | 0.949 | 0.024 | 0.973 | |
Y | 0.064 | 0.002 | 0.066 | |
align_CellType | 0.000 | 0.000 | 0.001 | |
cal_F2 | 0.291 | 0.206 | 0.497 | |
cal_MSE | 0.207 | 0.010 | 0.218 | |
eval_Cluster | 0.003 | 0.000 | 0.003 | |
process_Y | 0.566 | 0.007 | 0.574 | |
setUp_BPPARAM | 0.479 | 0.003 | 0.483 | |
trueclass | 0.002 | 0.001 | 0.003 | |