Jack Zhu
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/SRAdb |
| git_branch: RELEASE_3_14 |
| git_last_commit: 519051c |
| git_last_commit_date: 2021-10-26 11:55:53 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:25 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
To the developers/maintainers of the SRAdb package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1873/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SRAdb 1.56.0 (landing page) Jack Zhu
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SRAdb |
| Version: 1.56.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SRAdb_1.56.0.tar.gz |
| StartedAt: 2022-04-13 03:32:32 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 03:34:05 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 92.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SRAdb.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SRAdb_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SRAdb.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SRAdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SRAdb' version '1.56.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
'C:/Users/biocbuild/bbs-3.14-bioc/meat/SRAdb.Rcheck/00check.log'
for details.
SRAdb.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SRAdb_1.56.0.tar.gz && rm -rf SRAdb.buildbin-libdir && mkdir SRAdb.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SRAdb.buildbin-libdir SRAdb_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SRAdb_1.56.0.zip && rm SRAdb_1.56.0.tar.gz SRAdb_1.56.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
66 555k 66 368k 0 0 896k 0 --:--:-- --:--:-- --:--:-- 895k
100 555k 100 555k 0 0 690k 0 --:--:-- --:--:-- --:--:-- 690k
install for i386
* installing *source* package 'SRAdb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SRAdb'
finding HTML links ... done
IGVclear html
IGVcollapse html
IGVgenome html
IGVgoto html
IGVload html
IGVsession html
IGVsnapshot html
IGVsocket html
IGVsort html
SRAdb-package html
ascpR html
ascpSRA html
colDescriptions html
entityGraph html
getFASTQfile html
getFASTQinfo html
getSRA html
getSRAdbFile html
getSRAfile html
getSRAinfo html
listSRAfile html
sraConvert html
sraGraph html
startIGV html
** 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
install for x64
* installing *source* package 'SRAdb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SRAdb' as SRAdb_1.56.0.zip
* DONE (SRAdb)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SRAdb' successfully unpacked and MD5 sums checked
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SRAdb.Rcheck/examples_i386/SRAdb-Ex.timings
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SRAdb.Rcheck/examples_x64/SRAdb-Ex.timings
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