Colin A. Smith
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/annaffy |
| git_branch: RELEASE_3_13 |
| git_last_commit: e4b2445 |
| git_last_commit_date: 2021-06-19 21:06:30 -0400 (Sat, 19 Jun 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:57 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the annaffy package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annaffy.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 59/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| annaffy 1.64.2 (landing page) Colin A. Smith
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: annaffy |
| Version: 1.64.2 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings annaffy_1.64.2.tar.gz |
| StartedAt: 2021-10-14 19:30:01 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 19:32:45 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 163.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: annaffy.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:annaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings annaffy_1.64.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/annaffy.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annaffy/DESCRIPTION' ... OK
* this is package 'annaffy' version '1.64.2'
* 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 'annaffy' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmpkd7IUn/R.INSTALL15e067665ebf/annaffy/man/getURL-methods.Rd:25: missing link 'aafUniGene-class'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/annaffy.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 ... 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 'methods' which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' call to 'tcltk' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'Biobase' 'BiocManager' 'GO.db' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': 'BiocManager:::available'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'annaffy/R/zzz.R':
.onLoad calls:
require(methods)
Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
.aaf.goterm: no visible binding for global variable 'GOTERM'
aafGO: no visible global function definition for 'GO_dbfile'
aafTableInt: no visible global function definition for 'sampleNames'
aafTableInt: no visible global function definition for 'featureNames'
aafTableInt: no visible global function definition for 'exprs'
chkPkgs: no visible global function definition for 'userQuery'
selectorWidget : move: no visible global function definition for
'tkcurselection'
selectorWidget : move: no visible global function definition for
'tclvalue'
selectorWidget : move: no visible global function definition for
'tkget'
selectorWidget : move: no visible global function definition for
'tkinsert'
selectorWidget : move: no visible global function definition for
'tkdelete'
selectorWidget : move: no visible global function definition for
'tkselection.clear'
selectorWidget : ok: no visible global function definition for 'tkget'
selectorWidget : ok: no visible global function definition for
'tkdestroy'
selectorWidget: no visible global function definition for 'tktoplevel'
selectorWidget: no visible global function definition for 'tkwm.title'
selectorWidget: no visible global function definition for
'tkwm.resizable'
selectorWidget: no visible global function definition for 'tkframe'
selectorWidget: no visible global function definition for 'tklistbox'
selectorWidget : <anonymous>: no visible global function definition for
'tkset'
selectorWidget: no visible global function definition for 'tkscrollbar'
selectorWidget : <anonymous>: no visible global function definition for
'tkyview'
selectorWidget: no visible global function definition for 'tkgrid'
selectorWidget: no visible global function definition for 'tklabel'
selectorWidget: no visible global function definition for 'tkbutton'
selectorWidget: no visible global function definition for 'tkinsert'
selectorWidget : <anonymous>: no visible global function definition for
'tkdestroy'
selectorWidget: no visible global function definition for 'tkbind'
selectorWidget: no visible global function definition for
'tkwait.window'
saveHTML,aafTable: no visible global function definition for
'browseURL'
Undefined global functions or variables:
GOTERM GO_dbfile browseURL exprs featureNames sampleNames tclvalue
tkbind tkbutton tkcurselection tkdelete tkdestroy tkframe tkget
tkgrid tkinsert tklabel tklistbox tkscrollbar tkselection.clear tkset
tktoplevel tkwait.window tkwm.resizable tkwm.title tkyview userQuery
Consider adding
importFrom("utils", "browseURL")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'getURL-methods.Rd':
'aafUniGene-class'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
is.annpkg 5.7 1.34 7.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
is.annpkg 6.38 0.95 7.33
* 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: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/annaffy.Rcheck/00check.log'
for details.
annaffy.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/annaffy_1.64.2.tar.gz && rm -rf annaffy.buildbin-libdir && mkdir annaffy.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=annaffy.buildbin-libdir annaffy_1.64.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL annaffy_1.64.2.zip && rm annaffy_1.64.2.tar.gz annaffy_1.64.2.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
100 71271 100 71271 0 0 450k 0 --:--:-- --:--:-- --:--:-- 451k
install for i386
* installing *source* package 'annaffy' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'annaffy'
finding HTML links ... done
aaf.character html
aaf.goterm html
aaf.handler html
aaf.integer html
aaf.raw html
aafChromLoc-class html
aafChromLoc html
aafChromosome-class html
aafChromosome html
aafCytoband-class html
aafCytoband html
aafDescription-class html
aafDescription html
aafExpr html
aafGO-class html
aafGO html
aafGOItem-class html
aafGenBank-class html
aafGenBank html
aafIntensity-class html
aafList-class html
aafLocusLink-class html
aafLocusLink html
aafPathway-class html
aafPathway html
aafPathwayItem-class html
aafProbe-class html
aafProbe html
aafPubMed-class html
aafPubMed html
aafSearchGO html
aafSearchText html
aafSigned-class html
aafSymbol-class html
aafSymbol html
aafTable-class html
aafTable html
aafTableAnn html
aafTableFrame html
aafTableInt html
chkPkgs html
getCSS-methods html
getHTML-methods html
getTD-methods html
getText-methods html
getURL-methods html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmpkd7IUn/R.INSTALL15e067665ebf/annaffy/man/getURL-methods.Rd:25: missing link 'aafUniGene-class'
is.annpkg html
selectorWidget 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 'annaffy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annaffy' as annaffy_1.64.2.zip
* DONE (annaffy)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'annaffy' successfully unpacked and MD5 sums checked
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annaffy.Rcheck/examples_i386/annaffy-Ex.timings
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annaffy.Rcheck/examples_x64/annaffy-Ex.timings
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