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 12:04 -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 1924/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seq2pathway 1.38.0 (landing page) Arjun Kinstlick
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the seq2pathway package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seq2pathway.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: seq2pathway |
Version: 1.38.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seq2pathway.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seq2pathway_1.38.0.tar.gz |
StartedAt: 2024-12-20 05:24:21 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:28:27 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 245.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: seq2pathway.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seq2pathway.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seq2pathway_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/seq2pathway.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 ‘seq2pathway/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seq2pathway’ version ‘1.38.0’ * 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 ... NOTE Found the following hidden files and directories: vignettes/.RData These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘seq2pathway’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/seq2pathway.Rcheck/00install.out’ for details. * 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION Most likely ‘inst/CITATION’ should be used instead. * 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 ... WARNING 'library' or 'require' call not declared from: ‘biomaRt’ 'library' or 'require' call to ‘biomaRt’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE FAIME_EmpiricalP: no visible global function definition for ‘data’ FAIME_EmpiricalP: no visible binding for global variable ‘gencode_coding’ FisherTest_GO_BP_MF_CC: no visible global function definition for ‘data’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_BP_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_MF_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_CC_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘Des_BP_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘Des_MF_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘Des_CC_list’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_GENCODE_df_hg_v36’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_GENCODE_df_hg_v19’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_GENCODE_df_mm_vM25’ FisherTest_GO_BP_MF_CC: no visible binding for global variable ‘GO_GENCODE_df_mm_vM1’ FisherTest_MsigDB: no visible global function definition for ‘data’ FisherTest_MsigDB: no visible binding for global variable ‘Msig_GENCODE_df_hg_v36’ FisherTest_MsigDB: no visible binding for global variable ‘Msig_GENCODE_df_hg_v19’ FisherTest_MsigDB: no visible binding for global variable ‘Msig_GENCODE_df_mm_vM25’ FisherTest_MsigDB: no visible binding for global variable ‘Msig_GENCODE_df_mm_vM1’ KSrank_EmpiricalP: no visible global function definition for ‘data’ KSrank_EmpiricalP: no visible binding for global variable ‘gencode_coding’ Normalize_F: no visible global function definition for ‘head’ cumulativerank_EmpiricalP: no visible global function definition for ‘data’ cumulativerank_EmpiricalP: no visible binding for global variable ‘gencode_coding’ gene2pathway_test: no visible global function definition for ‘data’ gene2pathway_test: no visible binding for global variable ‘GO_BP_list’ gene2pathway_test: no visible binding for global variable ‘GO_MF_list’ gene2pathway_test: no visible binding for global variable ‘GO_CC_list’ gene2pathway_test: no visible binding for global variable ‘Des_BP_list’ gene2pathway_test: no visible binding for global variable ‘Des_CC_list’ gene2pathway_test: no visible binding for global variable ‘Des_MF_list’ plotTop10: no visible binding for global variable ‘Fisher_odds’ plotTop10: no visible binding for global variable ‘FDR’ plotTop10: no visible global function definition for ‘barplot’ plotTop10: no visible global function definition for ‘lines’ plotTop10: no visible global function definition for ‘text’ plotTop10: no visible global function definition for ‘abline’ rungene2pathway_EmpiricalP: no visible global function definition for ‘txtProgressBar’ rungene2pathway_EmpiricalP: no visible global function definition for ‘setTxtProgressBar’ runseq2gene: no visible global function definition for ‘write.table’ runseq2gene: no visible global function definition for ‘read.table’ runseq2pathway: no visible global function definition for ‘data’ runseq2pathway: no visible binding for global variable ‘GO_BP_list’ runseq2pathway: no visible binding for global variable ‘GO_MF_list’ runseq2pathway: no visible binding for global variable ‘GO_CC_list’ runseq2pathway: no visible binding for global variable ‘Des_BP_list’ runseq2pathway: no visible binding for global variable ‘Des_CC_list’ runseq2pathway: no visible binding for global variable ‘Des_MF_list’ runseq2pathway: no visible global function definition for ‘write.table’ runseq2pathway: no visible global function definition for ‘read.table’ Undefined global functions or variables: Des_BP_list Des_CC_list Des_MF_list FDR Fisher_odds GO_BP_list GO_CC_list GO_GENCODE_df_hg_v19 GO_GENCODE_df_hg_v36 GO_GENCODE_df_mm_vM1 GO_GENCODE_df_mm_vM25 GO_MF_list Msig_GENCODE_df_hg_v19 Msig_GENCODE_df_hg_v36 Msig_GENCODE_df_mm_vM1 Msig_GENCODE_df_mm_vM25 abline barplot data gencode_coding head lines read.table setTxtProgressBar text txtProgressBar write.table Consider adding importFrom("graphics", "abline", "barplot", "lines", "text") importFrom("utils", "data", "head", "read.table", "setTxtProgressBar", "txtProgressBar", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) runseq2gene.Rd:22-24: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:25-27: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:28-30: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:31-34: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:35-37: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:41-43: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:44-46: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:47-49: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:50-52: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2gene.Rd:112-114: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:115-117: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:118-120: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:121-123: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:124-127: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:128-131: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:132-134: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:135-137: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2gene.Rd:138-140: Lost braces in \enumerate; \value handles \item{}{} directly checkRd: (-1) runseq2pathway.Rd:26-28: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:29-31: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:32-34: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:35-37: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:38-40: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:44-46: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:47-49: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:50-52: Lost braces in \enumerate; meant \describe ? checkRd: (-1) runseq2pathway.Rd:53-55: Lost braces in \enumerate; 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runseq2gene 26.521 1.174 27.709 runseq2pathway 26.285 1.111 27.397 * 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: 2 WARNINGs, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/seq2pathway.Rcheck/00check.log’ for details.
seq2pathway.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL seq2pathway ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘seq2pathway’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’ ** testing if installed package keeps a record of temporary installation path * DONE (seq2pathway)
seq2pathway.Rcheck/seq2pathway-Ex.timings
name | user | system | elapsed | |
Chipseq_Peak_demo | 0.554 | 0.000 | 0.554 | |
FisherTest_GO_BP_MF_CC | 2.699 | 0.039 | 2.738 | |
FisherTest_MsigDB | 2.049 | 0.080 | 2.130 | |
GRanges_demo | 0.001 | 0.000 | 0.001 | |
addDescription | 0.426 | 0.023 | 2.018 | |
dat_RNA | 0.012 | 0.000 | 0.012 | |
dat_chip | 0.001 | 0.000 | 0.001 | |
gene2pathway_test | 0.431 | 0.015 | 0.446 | |
plotTop10 | 3.246 | 0.060 | 3.306 | |
runseq2gene | 26.521 | 1.174 | 27.709 | |
runseq2pathway | 26.285 | 1.111 | 27.397 | |