Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 2011/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SRAdb 1.67.0 (landing page) Jack Zhu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the SRAdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SRAdb.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: SRAdb |
Version: 1.67.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SRAdb.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SRAdb_1.67.0.tar.gz |
StartedAt: 2024-06-10 10:33:39 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 10:38:38 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 298.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SRAdb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SRAdb.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SRAdb_1.67.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SRAdb.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SRAdb/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SRAdb' version '1.67.0' * 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: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'SRAdb' can be installed ... OK * 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 ... NOTE The following files look like leftovers: 'SRAdb/SRAdb-package.Rd' Please remove them from your package. * 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 ... NOTE 'library' or 'require' call to 'RCurl' which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: 'RSQLite' 'graph' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .socketWrite: no visible global function definition for 'write.socket' .socketWrite: no visible global function definition for 'read.socket' IGVsocket: no visible global function definition for 'make.socket' colDescriptions: no visible global function definition for 'dbGetQuery' entityGraph: no visible global function definition for 'na.omit' entityGraph: no visible global function definition for 'new' entityGraph : <anonymous>: no visible global function definition for 'addEdge' getFASTQfile: no visible global function definition for 'download.file' getFASTQinfo: no visible global function definition for 'dbGetQuery' getSRA: no visible global function definition for 'dbGetQuery' getSRAdbFile: no visible global function definition for 'download.file' getSRAdbFile: no visible global function definition for 'dbConnect' getSRAdbFile: no visible global function definition for 'SQLite' getSRAdbFile: no visible global function definition for 'dbGetQuery' getSRAdbFile: no visible global function definition for 'dbDisconnect' getSRAfile: no visible global function definition for 'download.file' getSRAinfo: no visible global function definition for 'na.omit' sraConvert: no visible global function definition for 'dbGetQuery' startIGV: no visible global function definition for 'browseURL' Undefined global functions or variables: SQLite addEdge browseURL dbConnect dbDisconnect dbGetQuery download.file make.socket na.omit new read.socket write.socket Consider adding importFrom("methods", "new") importFrom("stats", "na.omit") importFrom("utils", "browseURL", "download.file", "make.socket", "read.socket", "write.socket") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * 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/SRAdb.Rcheck/00check.log' for details.
SRAdb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SRAdb ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'SRAdb' ... ** using staged installation ** R ** 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 (SRAdb)
SRAdb.Rcheck/SRAdb-Ex.timings
name | user | system | elapsed | |
IGVclear | 0 | 0 | 0 | |
IGVcollapse | 0 | 0 | 0 | |
IGVgenome | 0 | 0 | 0 | |
IGVgoto | 0 | 0 | 0 | |
IGVload | 0 | 0 | 0 | |
IGVsession | 0 | 0 | 0 | |
IGVsnapshot | 0 | 0 | 0 | |
IGVsocket | 0 | 0 | 0 | |
IGVsort | 0 | 0 | 0 | |
SRAdb-package | 0.12 | 0.02 | 0.16 | |
ascpR | 0 | 0 | 0 | |
ascpSRA | 0 | 0 | 0 | |
colDescriptions | 0.03 | 0.00 | 0.03 | |
entityGraph | 0.02 | 0.00 | 0.01 | |
getFASTQfile | 0 | 0 | 0 | |
getFASTQinfo | 0 | 0 | 0 | |
getSRA | 0.03 | 0.00 | 0.03 | |
getSRAdbFile | 0 | 0 | 0 | |
getSRAfile | 0 | 0 | 0 | |
getSRAinfo | 0.00 | 0.02 | 0.02 | |
listSRAfile | 0 | 0 | 0 | |
sraConvert | 0 | 0 | 0 | |
sraGraph | 0.41 | 0.40 | 0.89 | |
startIGV | 0 | 0 | 0 | |