| Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:18:21 -0400 (Wed, 15 Apr 2020).
| Package 694/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GEOmetadb 1.48.2 Jack Zhu
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: GEOmetadb |
| Version: 1.48.2 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GEOmetadb.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GEOmetadb_1.48.2.tar.gz |
| StartedAt: 2020-04-15 03:29:50 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:31:07 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 77.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GEOmetadb.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GEOmetadb.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GEOmetadb_1.48.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GEOmetadb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOmetadb' version '1.48.2'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
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 'GEOmetadb' can be installed ... WARNING
Found the following significant warnings:
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/GEOmetadb-package.Rd:52: unexpected END_OF_INPUT '
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/columnDescriptions.Rd:34: unexpected END_OF_INPUT '
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/geoConvert.Rd:38: unexpected section header '\keyword'
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/getBiocPlatformMap.Rd:36: unexpected END_OF_INPUT '
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/getSQLiteFile.Rd:37: unexpected section header '\keyword'
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getSQLiteFile: no visible global function definition for
'download.file'
Undefined global functions or variables:
download.file
Consider adding
importFrom("utils", "download.file")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: man/GEOmetadb-package.Rd:52: unexpected END_OF_INPUT '
'
prepare_Rd: man/columnDescriptions.Rd:34: unexpected END_OF_INPUT '
'
prepare_Rd: man/geoConvert.Rd:38: unexpected section header '\keyword'
prepare_Rd: man/getBiocPlatformMap.Rd:36: unexpected END_OF_INPUT '
'
prepare_Rd: man/getSQLiteFile.Rd:37: unexpected section header '\keyword'
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getSQLiteFile':
getSQLiteFile
Code: function(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz",
type = "full")
Docs: function(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz",
type = "normal")
Mismatches in argument default values:
Name: 'type' Code: "full" Docs: "normal"
* 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' ... ERROR
Running examples in 'GEOmetadb-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geoConvert
> ### Title: Cross-reference between GEO data types
> ### Aliases: geoConvert
>
> ### ** Examples
>
> ## Use the demo GEOmetadb database:
> if( !file.exists("GEOmetadb.sqlite") ) {
+ demo_sqlfile <- getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz", type = "demo")
+ } else {
+ demo_sqlfile <- "GEOmetadb.sqlite"
+ }
> ls = geoConvert('GPL96', out_type=c("GSE", 'GSM'), sqlite_db_name=demo_sqlfile)
> names(ls)
[1] "gse" "gsm"
> head(ls[[1]])
from_acc to_acc
1 GPL96 GSE1000
2 GPL96 GSE10072
3 GPL96 GSE10089
4 GPL96 GSE10137
5 GPL96 GSE10139
6 GPL96 GSE1017
>
> ## Download the full GEOmetadb database:
> ## Not run: geometadbfile <- getSQLiteFile()
>
> {IO}
Error: object 'IO' not found
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'GEOmetadb-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geoConvert
> ### Title: Cross-reference between GEO data types
> ### Aliases: geoConvert
>
> ### ** Examples
>
> ## Use the demo GEOmetadb database:
> if( !file.exists("GEOmetadb.sqlite") ) {
+ demo_sqlfile <- getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz", type = "demo")
+ } else {
+ demo_sqlfile <- "GEOmetadb.sqlite"
+ }
> ls = geoConvert('GPL96', out_type=c("GSE", 'GSM'), sqlite_db_name=demo_sqlfile)
> names(ls)
[1] "gse" "gsm"
> head(ls[[1]])
from_acc to_acc
1 GPL96 GSE1000
2 GPL96 GSE10072
3 GPL96 GSE10089
4 GPL96 GSE10137
5 GPL96 GSE10139
6 GPL96 GSE1017
>
> ## Download the full GEOmetadb database:
> ## Not run: geometadbfile <- getSQLiteFile()
>
> {IO}
Error: object 'IO' not found
Execution halted
* 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 ERRORs, 3 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb.Rcheck/00check.log'
for details.
GEOmetadb.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GEOmetadb_1.48.2.tar.gz && rm -rf GEOmetadb.buildbin-libdir && mkdir GEOmetadb.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GEOmetadb.buildbin-libdir GEOmetadb_1.48.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GEOmetadb_1.48.2.zip && rm GEOmetadb_1.48.2.tar.gz GEOmetadb_1.48.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 115k 100 115k 0 0 1100k 0 --:--:-- --:--:-- --:--:-- 1144k
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'GEOmetadb/vignettes/GEOmetadb.Rmd' to 'GEOmetadb/README.md'
* installing *source* package 'GEOmetadb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/GEOmetadb-package.Rd:52: unexpected END_OF_INPUT '
'
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/columnDescriptions.Rd:34: unexpected END_OF_INPUT '
'
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/geoConvert.Rd:38: unexpected section header '\keyword'
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/getBiocPlatformMap.Rd:36: unexpected END_OF_INPUT '
'
Warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpmgJqMD/R.INSTALL144c7f9c5733/GEOmetadb/man/getSQLiteFile.Rd:37: unexpected section header '\keyword'
*** installing help indices
converting help for package 'GEOmetadb'
finding HTML links ... done
GEOmetadb-package html
columnDescriptions html
geoConvert html
getBiocPlatformMap html
getSQLiteFile 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
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'GEOmetadb/vignettes/GEOmetadb.Rmd' to 'GEOmetadb/README.md'
* installing *source* package 'GEOmetadb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GEOmetadb' as GEOmetadb_1.48.2.zip
* DONE (GEOmetadb)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GEOmetadb' successfully unpacked and MD5 sums checked
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GEOmetadb.Rcheck/examples_i386/GEOmetadb-Ex.timings
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GEOmetadb.Rcheck/examples_x64/GEOmetadb-Ex.timings
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