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 12:03 -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 813/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genoCN 1.58.0 (landing page) Wei Sun
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
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 genoCN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genoCN.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: genoCN |
Version: 1.58.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:genoCN.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings genoCN_1.58.0.tar.gz |
StartedAt: 2024-12-20 00:13:39 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:17:57 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 258.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: genoCN.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:genoCN.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings genoCN_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/genoCN.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘genoCN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘genoCN’ version ‘1.58.0’ * 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' 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 ‘genoCN’ can be installed ... WARNING Found the following significant warnings: utility.c:155:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] See ‘/home/biocbuild/bbs-3.20-bioc/meat/genoCN.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 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 genoCNA: no visible binding for global variable ‘init.Para.CNA’ genoCNV: no visible binding for global variable ‘init.Para.CNV’ Undefined global functions or variables: init.Para.CNA init.Para.CNV * checking Rd files ... NOTE checkRd: (-1) genoCNA.Rd:60: Escaped LaTeX specials: \_ checkRd: (-1) genoCNA.Rd:61: Escaped LaTeX specials: \_ checkRd: (-1) genoCNV.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) init.Para.CNA.Rd:14-16: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:17-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:20-22: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:23-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:25-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:27-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:30-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:34-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:38-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:40-41: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:42-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:14-16: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:17-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:20-22: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:23-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:25-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:27-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:30-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:34-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:38-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:40-41: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:42-46: Lost braces in \itemize; meant \describe ? * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genoCNA 5.096 0.158 5.254 * 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, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/genoCN.Rcheck/00check.log’ for details.
genoCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL genoCN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘genoCN’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tnorm_mle.c -o tnorm_mle.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utility.c -o utility.o utility.c: In function ‘readfile’: utility.c:155:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(file,"%s",temp); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c xCNV.c -o xCNV.o xCNV.c: In function ‘emiss’: xCNV.c:317:25: warning: unused variable ‘k’ [-Wunused-variable] 317 | int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR; | ^ xCNV.c:317:16: warning: unused variable ‘K’ [-Wunused-variable] 317 | int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR; | ^ xCNV.c: In function ‘baum_welch’: xCNV.c:787:20: warning: unused variable ‘sd_b_tmp’ [-Wunused-variable] 787 | double mu_b_tmp, sd_b_tmp; | ^~~~~~~~ xCNV.c:787:10: warning: unused variable ‘mu_b_tmp’ [-Wunused-variable] 787 | double mu_b_tmp, sd_b_tmp; | ^~~~~~~~ xCNV.c:762:10: warning: variable ‘LL’ set but not used [-Wunused-but-set-variable] 762 | int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA, | ^~ xCNV.c:1753:17: warning: ‘pbf’ may be used uninitialized [-Wmaybe-uninitialized] 1753 | weights(ws, pbf, z, CNA, contam, nGtp, *geno_error); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xCNV.c:769:18: note: ‘pbf’ was declared here 769 | double ws[10], pbf, baf; | ^~~ xCNV.c:1753:17: warning: ‘nGtp’ may be used uninitialized [-Wmaybe-uninitialized] 1753 | weights(ws, pbf, z, CNA, contam, nGtp, *geno_error); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xCNV.c:768:31: note: ‘nGtp’ was declared here 768 | int k1s[4], rid[4], cid[4], nGtp; | ^~~~ gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o genoCN.so tnorm_mle.o utility.o xCNV.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-genoCN/00new/genoCN/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 (genoCN)
genoCN.Rcheck/genoCN-Ex.timings
name | user | system | elapsed | |
genoCNA | 5.096 | 0.158 | 5.254 | |
genoCNV | 2.207 | 0.031 | 2.238 | |
init.Para.CNA | 0.000 | 0.000 | 0.001 | |
init.Para.CNV | 0.001 | 0.000 | 0.001 | |
plotCN | 1.126 | 0.012 | 1.139 | |
snpData | 1.123 | 0.015 | 1.139 | |
snpInfo | 1.128 | 0.014 | 1.142 | |