Sean Davis
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/GEOquery |
| git_branch: RELEASE_3_13 |
| git_last_commit: 028b84d |
| git_last_commit_date: 2021-05-19 11:36:47 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the GEOquery package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GEOquery.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 757/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GEOquery 2.60.0 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GEOquery |
| Version: 2.60.0 |
| Command: chmod a+r GEOquery -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GEOquery |
| StartedAt: 2021-10-14 14:29:23 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 14:31:13 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 110.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r GEOquery -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GEOquery
###
##############################################################################
##############################################################################
* 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.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)
Rows: 22645 Columns: 19
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, IDENTIFIER
dbl (17): GSM11815, GSM11832, GSM12069, GSM12083, GSM12101, GSM12106, GSM122...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Reading file....
Parsing....
Found 36 entities...
GPL96 (1 of 37 entities)
GPL97 (2 of 37 entities)
GSM11805 (3 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM11810 (4 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM11814 (5 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM11815 (6 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM11823 (7 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM11827 (8 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM11830 (9 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM11832 (10 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12067 (11 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12069 (12 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12075 (13 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12078 (14 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12079 (15 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12083 (16 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12098 (17 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12099 (18 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12100 (19 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12101 (20 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12105 (21 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12106 (22 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12268 (23 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12269 (24 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12270 (25 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12274 (26 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12283 (27 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12287 (28 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12298 (29 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12299 (30 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12300 (31 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12301 (32 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12399 (33 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12412 (34 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12444 (35 of 37 entities)
Rows: 22283 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
GSM12448 (36 of 37 entities)
Rows: 22645 Columns: 3
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): ID_REF, ABS_CALL
dbl (1): VALUE
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
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
Rows: 12600 Columns: 182
-- Column specification --------------------------------------------------------
Delimiter: "\t"
dbl (182): ID_REF, GSM48681, GSM48682, GSM48683, GSM48684, GSM48685, GSM4868...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Warning: One or more parsing issues, see `problems()` for details
File stored at:
C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp6vLB4E/GPL1977.soft
Quitting from lines 135-139 (GEOquery.Rmd)
Error: processing vignette 'GEOquery.Rmd' failed with diagnostics:
invalid 'row.names' length
--- failed re-building 'GEOquery.Rmd'
SUMMARY: processing the following file failed:
'GEOquery.Rmd'
Error: Vignette re-building failed.
Execution halted