Package: GEOmetadb

Version: 1.48.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GEOmetadb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GEOmetadb_1.48.2.tar.gz

StartedAt: 2020-04-15 02:40:39 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:41:37 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 57.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: GEOmetadb.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GEOmetadb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GEOmetadb_1.48.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GEOmetadb’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/GEOmetadb-package.Rd:52: unexpected END_OF_INPUT '
  Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/columnDescriptions.Rd:34: unexpected END_OF_INPUT '
  Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/geoConvert.Rd:38: unexpected section header '\keyword'
  Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/getBiocPlatformMap.Rd:36: unexpected END_OF_INPUT '
  Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/getSQLiteFile.Rd:37: unexpected section header '\keyword'
See ‘/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
* 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 ... 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: 1 ERROR, 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GEOmetadb
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GEOmetadb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/GEOmetadb-package.Rd:52: unexpected END_OF_INPUT '
'
Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/columnDescriptions.Rd:34: unexpected END_OF_INPUT '
'
Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/geoConvert.Rd:38: unexpected section header '\keyword'
Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/getBiocPlatformMap.Rd:36: unexpected END_OF_INPUT '
'
Warning: /Users/biocbuild/bbs-3.10-bioc/meat/GEOmetadb/man/getSQLiteFile.Rd:37: unexpected section header '\keyword'
*** 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 (GEOmetadb)

name	user	system	elapsed
GEOmetadb-package	0.561	0.442	2.036
columnDescriptions	0.004	0.000	0.005