GEOquery 2.52.0
Sean Davis
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/GEOquery |
| Branch: RELEASE_3_9 |
| Last Commit: 3059331 |
| Last Changed Date: 2019-05-02 11:53:05 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | [ ERROR ] | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK |  |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GEOquery
###
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* checking for file ‘GEOquery/DESCRIPTION’ ... OK
* preparing ‘GEOquery’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GEOquery.Rmd’ using rmarkdown
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect,
is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, rank, rbind, 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)
Parsed with column specification:
cols(
ID_REF = col_character(),
IDENTIFIER = col_character(),
GSM11815 = col_double(),
GSM11832 = col_double(),
GSM12069 = col_double(),
GSM12083 = col_double(),
GSM12101 = col_double(),
GSM12106 = col_double(),
GSM12274 = col_double(),
GSM12299 = col_double(),
GSM12412 = col_double(),
GSM11810 = col_double(),
GSM11827 = col_double(),
GSM12078 = col_double(),
GSM12099 = col_double(),
GSM12269 = col_double(),
GSM12287 = col_double(),
GSM12301 = col_double(),
GSM12448 = col_double()
)
Reading file....
Parsing....
Found 36 entities...
GPL96 (1 of 37 entities)
Warning: 68 parsing failures.
row col expected actual file
22216 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
22217 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
22218 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
22219 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
22220 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
..... ....... .................. ......... ............
See problems(...) for more details.
GPL97 (2 of 37 entities)
Warning: 68 parsing failures.
row col expected actual file
22578 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
22579 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
22580 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
22581 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
22582 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
..... ....... .................. ......... ............
See problems(...) for more details.
GSM11805 (3 of 37 entities)
GSM11810 (4 of 37 entities)
GSM11814 (5 of 37 entities)
GSM11815 (6 of 37 entities)
GSM11823 (7 of 37 entities)
GSM11827 (8 of 37 entities)
GSM11830 (9 of 37 entities)
GSM11832 (10 of 37 entities)
GSM12067 (11 of 37 entities)
GSM12069 (12 of 37 entities)
GSM12075 (13 of 37 entities)
GSM12078 (14 of 37 entities)
GSM12079 (15 of 37 entities)
GSM12083 (16 of 37 entities)
GSM12098 (17 of 37 entities)
GSM12099 (18 of 37 entities)
GSM12100 (19 of 37 entities)
GSM12101 (20 of 37 entities)
GSM12105 (21 of 37 entities)
GSM12106 (22 of 37 entities)
GSM12268 (23 of 37 entities)
GSM12269 (24 of 37 entities)
GSM12270 (25 of 37 entities)
GSM12274 (26 of 37 entities)
GSM12283 (27 of 37 entities)
GSM12287 (28 of 37 entities)
GSM12298 (29 of 37 entities)
GSM12299 (30 of 37 entities)
GSM12300 (31 of 37 entities)
GSM12301 (32 of 37 entities)
GSM12399 (33 of 37 entities)
GSM12412 (34 of 37 entities)
GSM12444 (35 of 37 entities)
GSM12448 (36 of 37 entities)
Quitting from lines 135-139 (GEOquery.Rmd)
Error: processing vignette 'GEOquery.Rmd' failed with diagnostics:
HTTP error 404.
--- failed re-building ‘GEOquery.Rmd’
SUMMARY: processing the following file failed:
‘GEOquery.Rmd’
Error: Vignette re-building failed.
Execution halted