Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
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 994/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iCNV 1.27.0 (landing page) Zilu Zhou
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the iCNV package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iCNV.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: iCNV |
Version: 1.27.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iCNV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iCNV_1.27.0.tar.gz |
StartedAt: 2024-11-27 22:56:04 -0500 (Wed, 27 Nov 2024) |
EndedAt: 2024-11-27 23:02:46 -0500 (Wed, 27 Nov 2024) |
EllapsedTime: 402.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: iCNV.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iCNV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iCNV_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/iCNV.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘iCNV/DESCRIPTION’ ... OK * this is package ‘iCNV’ version ‘1.27.0’ * package encoding: UTF-8 * 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 ‘iCNV’ can be installed ... WARNING Found the following significant warnings: Note: break used in wrong context: no loop is visible See ‘/Users/biocbuild/bbs-3.21-bioc/meat/iCNV.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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 ... OK * 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 ... NOTE checkRd: (-1) iCNV_detection.Rd:31: Lost braces; missing escapes or markup? 31 | \item{visual}{An indicator variable with value {0,1,2}. 0 indicates no visualization, 1 indicates basic visualization, 2 indicates complete visualization (Note visual 2 only work for single platform and integer CN inferenced). Type integer. Default 0} | ^ checkRd: (-1) iCNV_detection.Rd:35: Lost braces; missing escapes or markup? 35 | \item{CN}{An indicator variable with value {0,1} for whether wants to infer exact copy number. 0 no exact CN, 1 exact CN. Type integer. Default 0.} | ^ checkRd: (-1) output_list.Rd:14: Lost braces; missing escapes or markup? 14 | \item{CN}{An indicator variable with value {0,1} for whether exact copy number inferred in iCNV_detection. 0 no exact CN, 1 exact CN. Type integer. Default 0.} | ^ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed iCNV_detection 7.239 0.322 7.593 * 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: 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/iCNV.Rcheck/00check.log’ for details.
iCNV.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iCNV ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘iCNV’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: break used in wrong context: no loop is visible ** 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 (iCNV)
iCNV.Rcheck/iCNV-Ex.timings
name | user | system | elapsed | |
bambaf_from_vcf | 3.071 | 0.157 | 3.256 | |
bed_generator | 0.107 | 0.005 | 0.113 | |
get_array_input | 0.034 | 0.014 | 0.053 | |
iCNV_detection | 7.239 | 0.322 | 7.593 | |
icnv_output_to_gb | 0.008 | 0.001 | 0.008 | |
normObj | 0.001 | 0.001 | 0.004 | |
output_list | 0.005 | 0.000 | 0.006 | |
plotHMMscore | 0.042 | 0.003 | 0.046 | |
plot_intensity | 0.035 | 0.005 | 0.039 | |
plotindi | 0.043 | 0.003 | 0.047 | |
qcObj | 0.000 | 0.000 | 0.001 | |