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### Running command:
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###   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
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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.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