Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 705/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FEAST 1.14.0 (landing page) Kenong Su
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.14.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FEAST.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings FEAST_1.14.0.tar.gz |
StartedAt: 2024-12-20 01:32:18 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:36:08 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 230.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FEAST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FEAST.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings FEAST_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/FEAST.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'FEAST/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'FEAST' version '1.14.0' * 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 whether package 'FEAST' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * checking installed package size ... NOTE installed size is 5.5Mb 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/FEAST/libs/x64/FEAST.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (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 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 'F:/biocbuild/bbs-3.20-bioc/meat/FEAST.Rcheck/00check.log' for details.
FEAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL FEAST ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'FEAST' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cal_3_metrics.c -o cal_3_metrics.o gcc -shared -s -static-libgcc -o FEAST.dll tmp.def cal_3_metrics.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-FEAST/00new/FEAST/libs/x64 ** 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 ** 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 | 2.00 | 0.05 | 3.10 | |
FEAST | 1.02 | 0.04 | 1.06 | |
FEAST_fast | 2.24 | 0.11 | 2.35 | |
Norm_Y | 0.23 | 0.02 | 0.25 | |
Select_Model_short_SC3 | 0.99 | 0.06 | 1.05 | |
Select_Model_short_TSCAN | 1.08 | 0.06 | 1.14 | |
TSCAN_Clust | 0 | 0 | 0 | |
Visual_Rslt | 1.23 | 0.08 | 1.56 | |
Y | 0.06 | 0.03 | 0.10 | |
align_CellType | 0 | 0 | 0 | |
cal_F2 | 0.64 | 0.31 | 0.95 | |
cal_MSE | 0.38 | 0.13 | 0.50 | |
eval_Cluster | 0.01 | 0.00 | 0.02 | |
process_Y | 0.75 | 0.07 | 0.82 | |
setUp_BPPARAM | 0.64 | 0.00 | 0.65 | |
trueclass | 0.00 | 0.02 | 0.01 | |