Wei Sun
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
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 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genoCN.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings genoCN_1.58.0.tar.gz |
| StartedAt: 2024-12-20 01:52:34 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 01:53:35 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 61.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: genoCN.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genoCN.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings genoCN_1.58.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/genoCN.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 '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 whether package 'genoCN' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/genoCN/libs/x64/genoCN.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 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
genoCNA 13.51 0.97 14.52
* 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
'F:/biocbuild/bbs-3.20-bioc/meat/genoCN.Rcheck/00check.log'
for details.
genoCN.Rcheck/00install.out
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### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL genoCN
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'genoCN' ...
** 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 tnorm_mle.c -o tnorm_mle.o
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 utility.c -o utility.o
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 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 -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.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-genoCN/00new/genoCN/libs/x64
** 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
** 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 | 13.51 | 0.97 | 14.52 | |
| genoCNV | 3.47 | 0.13 | 3.59 | |
| init.Para.CNA | 0.02 | 0.00 | 0.02 | |
| init.Para.CNV | 0 | 0 | 0 | |
| plotCN | 1.01 | 0.01 | 1.03 | |
| snpData | 1.10 | 0.05 | 1.14 | |
| snpInfo | 0.95 | 0.03 | 0.98 | |