Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:42 -0400 (Tue, 27 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" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 122/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BAGS 2.45.0 (landing page) Alejandro Quiroz-Zarate
| 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 BAGS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BAGS.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: BAGS |
Version: 2.45.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BAGS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BAGS_2.45.0.tar.gz |
StartedAt: 2024-08-26 18:57:36 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 18:58:44 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 67.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BAGS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BAGS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BAGS_2.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BAGS.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 ‘BAGS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BAGS’ version ‘2.45.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘BAGS’ 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 dependencies in R code ... NOTE Package in Depends field not imported from: ‘Biobase’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Gibbs2 15.420 0.926 16.461 MCMCDataSet 9.966 0.892 10.930 DataGeneSets 9.376 0.688 10.123 * 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-3.20-bioc/meat/BAGS.Rcheck/00check.log’ for details.
BAGS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BAGS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘BAGS’ ... ** 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 BAGS.c -o BAGS.o In file included from BAGS.c:8: ./FuncionesFast-Final.h:145:70: warning: unused variable 'YMu1' [-Wunused-variable] double media1,media,varianza1,varianza,resultado,varaux0,varaux1,YMu1; ^ ./FuncionesFast-Final.h:166:92: warning: unused variable 'C' [-Wunused-variable] double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff; ^ ./FuncionesFast-Final.h:166:94: warning: unused variable 'A' [-Wunused-variable] double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff; ^ ./FuncionesFast-Final.h:166:105: warning: unused variable 'MediaDiff' [-Wunused-variable] double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff; ^ BAGS.c:25:20: warning: unused variable 'escala2' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; ^ BAGS.c:25:12: warning: unused variable 'escala1' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; ^ BAGS.c:24:12: warning: unused variable 'formaAux' [-Wunused-variable] double formaAux; ^ BAGS.c:25:48: warning: unused variable 'resI' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; ^ BAGS.c:25:43: warning: unused variable 'rate' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; ^ BAGS.c:25:36: warning: unused variable 'escala' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; ^ BAGS.c:18:80: warning: variable 'ResSgmA' set but not used [-Wunused-but-set-variable] double ResRho1,ResRho2,ResRho3,ResRho4,ResSgmA1,ResSgmA2,ResSgmA3,ResSgmA4,ResSgmA; ^ BAGS.c:25:28: warning: unused variable 'escala3' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; ^ BAGS.c:15:15: warning: variable 'AaPi' set but not used [-Wunused-but-set-variable] double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2; ^ BAGS.c:332:15: warning: variable 'AaPi' set but not used [-Wunused-but-set-variable] double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2; ^ BAGS.c:335:63: warning: variable 'ResSgmA' set but not used [-Wunused-but-set-variable] double ResRho1,ResRho2,ResRho3,ResSgmA1,ResSgmA2,ResSgmA3,ResSgmA; ^ BAGS.c:342:43: warning: unused variable 'rate' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:342:48: warning: unused variable 'resI' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:342:28: warning: unused variable 'escala3' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:342:36: warning: unused variable 'escala' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:342:12: warning: unused variable 'escala1' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:342:20: warning: unused variable 'escala2' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:341:12: warning: unused variable 'formaAux' [-Wunused-variable] double formaAux; ^ BAGS.c:586:46: warning: variable 'ResSgmA' set but not used [-Wunused-but-set-variable] double ResRho1,ResRho2,ResSgmA1,ResSgmA2,ResSgmA; ^ BAGS.c:592:12: warning: unused variable 'formaAux' [-Wunused-variable] double formaAux; ^ BAGS.c:583:15: warning: variable 'AaPi' set but not used [-Wunused-but-set-variable] double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2; ^ BAGS.c:593:48: warning: unused variable 'resI' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:593:43: warning: unused variable 'rate' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:593:20: warning: unused variable 'escala2' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:593:12: warning: unused variable 'escala1' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:593:36: warning: unused variable 'escala' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:593:28: warning: unused variable 'escala3' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:786:36: warning: unused variable 'escala' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:786:28: warning: unused variable 'escala3' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:779:29: warning: variable 'ResSgmA' set but not used [-Wunused-but-set-variable] double ResRho1,ResSgmA1,ResSgmA; ^ BAGS.c:786:48: warning: unused variable 'resI' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:786:43: warning: unused variable 'rate' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:785:12: warning: unused variable 'formaAux' [-Wunused-variable] double formaAux; ^ BAGS.c:776:15: warning: variable 'AaPi' set but not used [-Wunused-but-set-variable] double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2; ^ BAGS.c:786:20: warning: unused variable 'escala2' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ BAGS.c:786:12: warning: unused variable 'escala1' [-Wunused-variable] double escala1,escala2,escala3,escala,rate,resI; // Aqui tengo duda ^ 40 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 BAGS.so BAGS.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-BAGS/00new/BAGS/libs ** R ** data ** 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 (BAGS)
BAGS.Rcheck/BAGS-Ex.timings
name | user | system | elapsed | |
AnnotationMFGO | 0.033 | 0.007 | 0.040 | |
BAGS-package | 0 | 0 | 0 | |
DataGeneSets | 9.376 | 0.688 | 10.123 | |
Gibbs2 | 15.420 | 0.926 | 16.461 | |
Gibbs3 | 0.000 | 0.000 | 0.001 | |
Gibbs4 | 0 | 0 | 0 | |
Gibbs5 | 0.000 | 0.001 | 0.000 | |
MCMCDataSet | 9.966 | 0.892 | 10.930 | |
ReadGMT | 0.000 | 0.001 | 0.001 | |