Wei Sun
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/genoCN |
| git_branch: RELEASE_3_20 |
| git_last_commit: f53faf3 |
| git_last_commit_date: 2024-10-29 09:33:31 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:35 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: genoCN |
| Version: 1.58.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:genoCN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings genoCN_1.58.0.tar.gz |
| StartedAt: 2025-04-01 06:46:28 -0000 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 06:47:05 -0000 (Tue, 01 Apr 2025) |
| EllapsedTime: 37.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: genoCN.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:genoCN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings genoCN_1.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/genoCN.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ... 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 ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 7.807 0.148 7.966
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/genoCN.Rcheck/00check.log’
for details.
genoCN.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL genoCN
###
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* installing to library ‘/home/biocbuild/R/R-4.4.3/site-library’
* installing *source* package ‘genoCN’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R-4.4.3/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c tnorm_mle.c -o tnorm_mle.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R-4.4.3/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c utility.c -o utility.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R-4.4.3/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,
| ^~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R-4.4.3/lib -L/usr/local/lib -o genoCN.so tnorm_mle.o utility.o xCNV.o -L/home/biocbuild/R/R-4.4.3/lib -lR
installing to /home/biocbuild/R/R-4.4.3/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 | 7.807 | 0.148 | 7.966 | |
| genoCNV | 2.872 | 0.028 | 2.903 | |
| init.Para.CNA | 0.001 | 0.000 | 0.001 | |
| init.Para.CNV | 0.001 | 0.000 | 0.001 | |
| plotCN | 1.138 | 0.012 | 1.152 | |
| snpData | 1.137 | 0.012 | 1.149 | |
| snpInfo | 1.139 | 0.008 | 1.149 | |