| Back to the "Multiple platform build/check report" | A B C D E F [G] H I J K L M N O P Q R S T U V W X Y Z |
This page was generated on 2017-08-16 13:19:07 -0400 (Wed, 16 Aug 2017).
| Package 552/1382 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| GEOquery 2.42.0 Sean Davis
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | ERROR | skipped | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: GEOquery |
| Version: 2.42.0 |
| Command: rm -rf GEOquery.buildbin-libdir GEOquery.Rcheck && mkdir GEOquery.buildbin-libdir GEOquery.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GEOquery.buildbin-libdir GEOquery_2.42.0.tar.gz >GEOquery.Rcheck\00install.out 2>&1 && cp GEOquery.Rcheck\00install.out GEOquery-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GEOquery.buildbin-libdir --install="check:GEOquery-install.out" --force-multiarch --no-vignettes --timings GEOquery_2.42.0.tar.gz |
| StartedAt: 2017-08-16 00:06:14 -0400 (Wed, 16 Aug 2017) |
| EndedAt: 2017-08-16 00:12:02 -0400 (Wed, 16 Aug 2017) |
| EllapsedTime: 347.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GEOquery.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf GEOquery.buildbin-libdir GEOquery.Rcheck && mkdir GEOquery.buildbin-libdir GEOquery.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GEOquery.buildbin-libdir GEOquery_2.42.0.tar.gz >GEOquery.Rcheck\00install.out 2>&1 && cp GEOquery.Rcheck\00install.out GEOquery-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GEOquery.buildbin-libdir --install="check:GEOquery-install.out" --force-multiarch --no-vignettes --timings GEOquery_2.42.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GEOquery.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GEOquery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOquery' version '2.42.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'GEOquery' can be installed ... OK
* checking installed package size ... NOTE
installed size is 13.8Mb
sub-directories of 1Mb or more:
extdata 12.8Mb
* 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 'limma' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Biobase'
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
File 'GEOquery/R/zzz.R':
.onLoad calls:
packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')")
packageStartupMessage("Setting options('GEOquery.inmemory.gpl'=FALSE)")
See section 'Good practice' in '?.onAttach'.
GDS2MA: no visible binding for global variable 'MA'
fastTabRead: no visible global function definition for 'read.table'
fastTabRead: no visible global function definition for 'read.delim'
getAndParseGSEMatrices: no visible global function definition for
'download.file'
getDirListing: no visible global function definition for 'read.table'
getGEOSuppFiles: no visible global function definition for
'download.file'
getGEOfile: no visible global function definition for 'download.file'
getGSEDataTables : <anonymous>: no visible global function definition
for 'read.delim'
parseGSEMatrix: no visible global function definition for 'read.table'
parseGSEMatrix: no visible global function definition for 'read.delim'
Undefined global functions or variables:
MA download.file read.delim read.table
Consider adding
importFrom("utils", "download.file", "read.delim", "read.table")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
cannot open destfile 'C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL//geo/series/GSE11nnn/GSE11413', reason 'No such file or directory'
Test files with failing tests
test_CaseMismatchedIDsGSE.R
testCaseMismatchedIDsGSE
test_EmptyGSE.R
testEmptyGSE
Error in BiocGenerics:::testPackage("GEOquery") :
unit tests failed for package GEOquery
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
ERROR in testCaseGSEgetGPLFALSE: Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open destfile 'C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59//geo/series/GSE2nnn/GSE2553', reason 'No such file or directory'
Test files with failing tests
test_SuppFileSupport.R
testSuppFileSupport
test_getGPLFALSE.R
testCaseGSEgetGPLFALSE
Error in BiocGenerics:::testPackage("GEOquery") :
unit tests failed for package GEOquery
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 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/GEOquery.Rcheck/00check.log'
for details.
runTests.Rout.fail:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("GEOquery")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35683/matrix/
OK
Found 2 file(s)
/geo/series/GSE35nnn/GSE35683/
Timing stopped at: 0.26 0.03 0.58
Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open destfile 'C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL//geo/series/GSE35nnn/GSE35683', reason 'No such file or directory'
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11413/matrix/
OK
Found 2 file(s)
/geo/series/GSE11nnn/GSE11413/
Timing stopped at: 0.31 0 0.44
Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open destfile 'C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL//geo/series/GSE11nnn/GSE11413', reason 'No such file or directory'
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GPL97.annot.gz
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GPL96.soft
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GSM11805.soft
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GPL4133.soft
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GSE1563.soft.gz
Parsing....
Found 63 entities...
GPL8300 (1 of 63 entities)
GSM26805 (2 of 63 entities)
GSM26806 (3 of 63 entities)
GSM26807 (4 of 63 entities)
GSM26808 (5 of 63 entities)
GSM26809 (6 of 63 entities)
GSM26810 (7 of 63 entities)
GSM26811 (8 of 63 entities)
GSM26812 (9 of 63 entities)
GSM26813 (10 of 63 entities)
GSM26814 (11 of 63 entities)
GSM26815 (12 of 63 entities)
GSM26816 (13 of 63 entities)
GSM26817 (14 of 63 entities)
GSM26818 (15 of 63 entities)
GSM26819 (16 of 63 entities)
GSM26820 (17 of 63 entities)
GSM26821 (18 of 63 entities)
GSM26822 (19 of 63 entities)
GSM26823 (20 of 63 entities)
GSM26824 (21 of 63 entities)
GSM26825 (22 of 63 entities)
GSM26826 (23 of 63 entities)
GSM26827 (24 of 63 entities)
GSM26828 (25 of 63 entities)
GSM26829 (26 of 63 entities)
GSM26830 (27 of 63 entities)
GSM26831 (28 of 63 entities)
GSM26832 (29 of 63 entities)
GSM26833 (30 of 63 entities)
GSM26834 (31 of 63 entities)
GSM26835 (32 of 63 entities)
GSM26836 (33 of 63 entities)
GSM26837 (34 of 63 entities)
GSM26838 (35 of 63 entities)
GSM26839 (36 of 63 entities)
GSM26840 (37 of 63 entities)
GSM26841 (38 of 63 entities)
GSM26842 (39 of 63 entities)
GSM26843 (40 of 63 entities)
GSM26844 (41 of 63 entities)
GSM26845 (42 of 63 entities)
GSM26846 (43 of 63 entities)
GSM26847 (44 of 63 entities)
GSM26848 (45 of 63 entities)
GSM26849 (46 of 63 entities)
GSM26850 (47 of 63 entities)
GSM26851 (48 of 63 entities)
GSM26852 (49 of 63 entities)
GSM26853 (50 of 63 entities)
GSM26854 (51 of 63 entities)
GSM26855 (52 of 63 entities)
GSM26856 (53 of 63 entities)
GSM26857 (54 of 63 entities)
GSM26858 (55 of 63 entities)
GSM26859 (56 of 63 entities)
GSM26860 (57 of 63 entities)
GSM26861 (58 of 63 entities)
GSM26862 (59 of 63 entities)
GSM26863 (60 of 63 entities)
GSM26864 (61 of 63 entities)
GSM26865 (62 of 63 entities)
GSM26866 (63 of 63 entities)
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GPL15505.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/
OK
Found 2 file(s)
GSE34145-GPL15796_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/GSE34145-GPL15796_series_matrix.txt.gz'
Content type 'application/x-gzip' length 6643 bytes
==================================================
downloaded 6643 bytes
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GPL15796.soft
GSE34145-GPL6102_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/GSE34145-GPL6102_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1428433 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GPL6102.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/
OK
Found 2 file(s)
GSE11595-GPL3906_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/GSE11595-GPL3906_series_matrix.txt.gz'
Content type 'application/x-gzip' length 59663 bytes (58 KB)
==================================================
downloaded 58 KB
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GPL3906.soft
GSE11595-GPL4348_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/GSE11595-GPL4348_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1528930 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GPL4348.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl/
OK
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl//GSE1000_RAW.tar'
Content type 'application/x-tar' length 35307520 bytes (33.7 MB)
==================================================
downloaded 33.7 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl//filelist.txt'
Content type 'text/plain' length 621 bytes
==================================================
downloaded 621 bytes
https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl/
OK
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz'
Content type 'application/x-gzip' length 3507725 bytes (3.3 MB)
==================================================
downloaded 3.3 MB
https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl/
OK
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz'
Content type 'application/x-gzip' length 3507725 bytes (3.3 MB)
==================================================
downloaded 3.3 MB
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL/GDS10.soft.gz
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/
OK
Found 1 file(s)
GSE2553_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/GSE2553_series_matrix.txt.gz'
Content type 'application/x-gzip' length 8480960 bytes (8.1 MB)
==================================================
downloaded 8.1 MB
RUNIT TEST PROTOCOL -- Wed Aug 16 00:09:54 2017
***********************************************
Number of test functions: 14
Number of errors: 2
Number of failures: 0
1 Test Suite :
GEOquery RUnit Tests - 14 test functions, 2 errors, 0 failures
ERROR in testCaseMismatchedIDsGSE: Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open destfile 'C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL//geo/series/GSE35nnn/GSE35683', reason 'No such file or directory'
ERROR in testEmptyGSE: Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open destfile 'C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpOclwaL//geo/series/GSE11nnn/GSE11413', reason 'No such file or directory'
Test files with failing tests
test_CaseMismatchedIDsGSE.R
testCaseMismatchedIDsGSE
test_EmptyGSE.R
testEmptyGSE
Error in BiocGenerics:::testPackage("GEOquery") :
unit tests failed for package GEOquery
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
runTests.Rout.fail:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("GEOquery")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35683/matrix/
OK
Found 1 file(s)
GSE35683_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35683/matrix/GSE35683_series_matrix.txt.gz'
Content type 'application/x-gzip' length 5733793 bytes (5.5 MB)
==================================================
downloaded 5.5 MB
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL570.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11413/matrix/
OK
Found 1 file(s)
GSE11413_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11413/matrix/GSE11413_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3997 bytes
==================================================
downloaded 3997 bytes
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL5082.soft
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL97.annot.gz
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL96.soft
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GSM11805.soft
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL4133.soft
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GSE1563.soft.gz
Parsing....
Found 63 entities...
GPL8300 (1 of 63 entities)
GSM26805 (2 of 63 entities)
GSM26806 (3 of 63 entities)
GSM26807 (4 of 63 entities)
GSM26808 (5 of 63 entities)
GSM26809 (6 of 63 entities)
GSM26810 (7 of 63 entities)
GSM26811 (8 of 63 entities)
GSM26812 (9 of 63 entities)
GSM26813 (10 of 63 entities)
GSM26814 (11 of 63 entities)
GSM26815 (12 of 63 entities)
GSM26816 (13 of 63 entities)
GSM26817 (14 of 63 entities)
GSM26818 (15 of 63 entities)
GSM26819 (16 of 63 entities)
GSM26820 (17 of 63 entities)
GSM26821 (18 of 63 entities)
GSM26822 (19 of 63 entities)
GSM26823 (20 of 63 entities)
GSM26824 (21 of 63 entities)
GSM26825 (22 of 63 entities)
GSM26826 (23 of 63 entities)
GSM26827 (24 of 63 entities)
GSM26828 (25 of 63 entities)
GSM26829 (26 of 63 entities)
GSM26830 (27 of 63 entities)
GSM26831 (28 of 63 entities)
GSM26832 (29 of 63 entities)
GSM26833 (30 of 63 entities)
GSM26834 (31 of 63 entities)
GSM26835 (32 of 63 entities)
GSM26836 (33 of 63 entities)
GSM26837 (34 of 63 entities)
GSM26838 (35 of 63 entities)
GSM26839 (36 of 63 entities)
GSM26840 (37 of 63 entities)
GSM26841 (38 of 63 entities)
GSM26842 (39 of 63 entities)
GSM26843 (40 of 63 entities)
GSM26844 (41 of 63 entities)
GSM26845 (42 of 63 entities)
GSM26846 (43 of 63 entities)
GSM26847 (44 of 63 entities)
GSM26848 (45 of 63 entities)
GSM26849 (46 of 63 entities)
GSM26850 (47 of 63 entities)
GSM26851 (48 of 63 entities)
GSM26852 (49 of 63 entities)
GSM26853 (50 of 63 entities)
GSM26854 (51 of 63 entities)
GSM26855 (52 of 63 entities)
GSM26856 (53 of 63 entities)
GSM26857 (54 of 63 entities)
GSM26858 (55 of 63 entities)
GSM26859 (56 of 63 entities)
GSM26860 (57 of 63 entities)
GSM26861 (58 of 63 entities)
GSM26862 (59 of 63 entities)
GSM26863 (60 of 63 entities)
GSM26864 (61 of 63 entities)
GSM26865 (62 of 63 entities)
GSM26866 (63 of 63 entities)
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL15505.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/
OK
Found 2 file(s)
GSE34145-GPL15796_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/GSE34145-GPL15796_series_matrix.txt.gz'
Content type 'application/x-gzip' length 6643 bytes
==================================================
downloaded 6643 bytes
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL15796.soft
GSE34145-GPL6102_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/GSE34145-GPL6102_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1428433 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL6102.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/
OK
Found 2 file(s)
GSE11595-GPL3906_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/GSE11595-GPL3906_series_matrix.txt.gz'
Content type 'application/x-gzip' length 59663 bytes (58 KB)
==================================================
downloaded 58 KB
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL3906.soft
GSE11595-GPL4348_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/GSE11595-GPL4348_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1528930 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GPL4348.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl/
OK
Timing stopped at: 0.04 0 0.23
Error in download.file(file.path(url, i), destfile = file.path(storedir, :
cannot open destfile 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GEOquery.Rcheck/tests_x64/GSE1000//geo/series/GSE1nnn/GSE1000', reason 'No such file or directory'
In addition: There were 50 or more warnings (use warnings() to see the first 50)
File stored at:
C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59/GDS10.soft.gz
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/
OK
Found 2 file(s)
/geo/series/GSE2nnn/GSE2553/
Timing stopped at: 0.04 0.02 0.19
Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open destfile 'C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59//geo/series/GSE2nnn/GSE2553', reason 'No such file or directory'
RUNIT TEST PROTOCOL -- Wed Aug 16 00:11:56 2017
***********************************************
Number of test functions: 14
Number of errors: 2
Number of failures: 0
1 Test Suite :
GEOquery RUnit Tests - 14 test functions, 2 errors, 0 failures
ERROR in testSuppFileSupport: Error in download.file(file.path(url, i), destfile = file.path(storedir, :
cannot open destfile 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GEOquery.Rcheck/tests_x64/GSE1000//geo/series/GSE1nnn/GSE1000', reason 'No such file or directory'
ERROR in testCaseGSEgetGPLFALSE: Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open destfile 'C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpykmB59//geo/series/GSE2nnn/GSE2553', reason 'No such file or directory'
Test files with failing tests
test_SuppFileSupport.R
testSuppFileSupport
test_getGPLFALSE.R
testCaseGSEgetGPLFALSE
Error in BiocGenerics:::testPackage("GEOquery") :
unit tests failed for package GEOquery
Execution halted
GEOquery.Rcheck/00install.out:
install for i386 * installing *source* package 'GEOquery' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'GEOquery' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GEOquery' as GEOquery_2.42.0.zip * DONE (GEOquery)
GEOquery.Rcheck/examples_i386/GEOquery-Ex.timings:
| name | user | system | elapsed | |
| GDS2MA | 0 | 0 | 0 | |
| getGEO | 0 | 0 | 0 | |
| getGEOSuppFiles | 0 | 0 | 0 | |
| getGEOfile | 0 | 0 | 0 | |
| getGSEDataTables | 0.51 | 0.06 | 0.88 | |
GEOquery.Rcheck/examples_x64/GEOquery-Ex.timings:
| name | user | system | elapsed | |
| GDS2MA | 0 | 0 | 0 | |
| getGEO | 0 | 0 | 0 | |
| getGEOSuppFiles | 0 | 0 | 0 | |
| getGEOfile | 0 | 0 | 0 | |
| getGSEDataTables | 0.50 | 0.10 | 0.86 | |