CRAN Package Check Results for Package GREP2

Last updated on 2018-11-24 00:51:08 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.1 31.71 345.56 377.27 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.1 28.34 282.72 311.06 ERROR
r-devel-linux-x86_64-fedora-clang 1.0.1 246.40 ERROR
r-devel-linux-x86_64-fedora-gcc 1.0.1 241.83 ERROR
r-devel-windows-ix86+x86_64 1.0.1 68.00 434.00 502.00 OK
r-patched-linux-x86_64 1.0.1 26.28 341.32 367.60 ERROR
r-patched-solaris-x86 1.0.1 601.40 ERROR
r-release-linux-x86_64 1.0.1 24.38 330.71 355.09 ERROR
r-release-windows-ix86+x86_64 1.0.1 69.00 425.00 494.00 OK
r-release-osx-x86_64 1.0.1 ERROR
r-oldrel-windows-ix86+x86_64 1.0.1 1.00 6.00 7.00 ERROR
r-oldrel-osx-x86_64 1.0.1 ERROR

Check Details

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘GREP2-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: get_metadata
    > ### Title: Download metadata from GEO and SRA
    > ### Aliases: get_metadata
    >
    > ### ** Examples
    >
    >
    > get_metadata(geo_series_acc="GSE102170",destdir=tempdir(),
    + geo_only=TRUE,download_method="auto")
    File stored at:
    /tmp/RtmpOwEtIU/GSE102170.soft.gz
    Reading file....
    Parsing....
    Found 3 entities...
    GPL15520 (1 of 4 entities)
    GSM2729816 (2 of 4 entities)
    GSM2729817 (3 of 4 entities)
    trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102170/matrix/GSE102170_series_matrix.txt.gz'
    Content type 'application/x-gzip' length 1764 bytes
    ==================================================
    downloaded 1764 bytes
    
    Parsed with column specification:
    cols()
    Error in .subset2(x, i) : subscript out of bounds
    Calls: get_metadata ... getGEO -> parseGEO -> parseGSEMatrix -> [[ -> [[.tbl_df
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘GREP2-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: get_metadata
    > ### Title: Download metadata from GEO and SRA
    > ### Aliases: get_metadata
    >
    > ### ** Examples
    >
    >
    > get_metadata(geo_series_acc="GSE102170",destdir=tempdir(),
    + geo_only=TRUE,download_method="auto")
    File stored at:
    /home/hornik/tmp/scratch/RtmpOISPfB/GSE102170.soft.gz
    Reading file....
    Parsing....
    Found 3 entities...
    GPL15520 (1 of 4 entities)
    GSM2729816 (2 of 4 entities)
    GSM2729817 (3 of 4 entities)
    trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102170/matrix/GSE102170_series_matrix.txt.gz'
    Content type 'application/x-gzip' length 1764 bytes
    ==================================================
    downloaded 1764 bytes
    
    Parsed with column specification:
    cols()
    Error in .subset2(x, i) : subscript out of bounds
    Calls: get_metadata ... getGEO -> parseGEO -> parseGSEMatrix -> [[ -> [[.tbl_df
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘GREP2-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: get_metadata
    > ### Title: Download metadata from GEO and SRA
    > ### Aliases: get_metadata
    >
    > ### ** Examples
    >
    >
    > get_metadata(geo_series_acc="GSE102170",destdir=tempdir(),
    + geo_only=TRUE,download_method="auto")
    File stored at:
    /tmp/Rtmp3dbxhN/GSE102170.soft.gz
    Reading file....
    Parsing....
    Found 3 entities...
    GPL15520 (1 of 4 entities)
    GSM2729816 (2 of 4 entities)
    GSM2729817 (3 of 4 entities)
    trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102170/matrix/GSE102170_series_matrix.txt.gz'
    Content type 'application/x-gzip' length 1764 bytes
    ==================================================
    downloaded 1764 bytes
    
    Parsed with column specification:
    cols()
    Error in .subset2(x, i) : subscript out of bounds
    Calls: get_metadata ... getGEO -> parseGEO -> parseGSEMatrix -> [[ -> [[.tbl_df
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘GREP2-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: get_metadata
    > ### Title: Download metadata from GEO and SRA
    > ### Aliases: get_metadata
    >
    > ### ** Examples
    >
    >
    > get_metadata(geo_series_acc="GSE102170",destdir=tempdir(),
    + geo_only=TRUE,download_method="auto")
    File stored at:
    /tmp/RtmpcT01xt/GSE102170.soft.gz
    Reading file....
    Parsing....
    Found 3 entities...
    GPL15520 (1 of 4 entities)
    GSM2729816 (2 of 4 entities)
    GSM2729817 (3 of 4 entities)
    trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102170/matrix/GSE102170_series_matrix.txt.gz'
    Content type 'application/x-gzip' length 1764 bytes
    ==================================================
    downloaded 1764 bytes
    
    Parsed with column specification:
    cols()
    Error in .subset2(x, i) : subscript out of bounds
    Calls: get_metadata ... getGEO -> parseGEO -> parseGSEMatrix -> [[ -> [[.tbl_df
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘GREP2-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: get_metadata
    > ### Title: Download metadata from GEO and SRA
    > ### Aliases: get_metadata
    >
    > ### ** Examples
    >
    >
    > get_metadata(geo_series_acc="GSE102170",destdir=tempdir(),
    + geo_only=TRUE,download_method="auto")
    File stored at:
    /tmp/RtmprAAeFe/GSE102170.soft.gz
    Reading file....
    Parsing....
    Found 3 entities...
    GPL15520 (1 of 4 entities)
    GSM2729816 (2 of 4 entities)
    GSM2729817 (3 of 4 entities)
    trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102170/matrix/GSE102170_series_matrix.txt.gz'
    Content type 'application/x-gzip' length 1764 bytes
    ==================================================
    downloaded 1764 bytes
    
    Parsed with column specification:
    cols()
    Error in .subset2(x, i) : subscript out of bounds
    Calls: get_metadata ... getGEO -> parseGEO -> parseGSEMatrix -> [[ -> [[.tbl_df
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘GREP2-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: get_metadata
    > ### Title: Download metadata from GEO and SRA
    > ### Aliases: get_metadata
    >
    > ### ** Examples
    >
    >
    > get_metadata(geo_series_acc="GSE102170",destdir=tempdir(),
    + geo_only=TRUE,download_method="auto")
    File stored at:
    /tmp/Rtmpp.a4mU/GSE102170.soft.gz
    Reading file....
    Parsing....
    Found 3 entities...
    GPL15520 (1 of 4 entities)
    GSM2729816 (2 of 4 entities)
    GSM2729817 (3 of 4 entities)
    trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102170/matrix/GSE102170_series_matrix.txt.gz'
    Content type 'application/x-gzip' length 1764 bytes
    ==================================================
    downloaded 1764 bytes
    
    Parsed with column specification:
    cols()
    Error in .subset2(x, i) : subscript out of bounds
    Calls: get_metadata ... getGEO -> parseGEO -> parseGSEMatrix -> [[ -> [[.tbl_df
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘GREP2-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: get_metadata
    > ### Title: Download metadata from GEO and SRA
    > ### Aliases: get_metadata
    >
    > ### ** Examples
    >
    >
    > get_metadata(geo_series_acc="GSE102170",destdir=tempdir(),
    + geo_only=TRUE,download_method="auto")
    File stored at:
    /tmp/RtmplXj2LZ/GSE102170.soft.gz
    Reading file....
    Parsing....
    Found 3 entities...
    GPL15520 (1 of 4 entities)
    GSM2729816 (2 of 4 entities)
    GSM2729817 (3 of 4 entities)
    trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102170/matrix/GSE102170_series_matrix.txt.gz'
    Content type 'application/x-gzip' length 1764 bytes
    ==================================================
    downloaded 1764 bytes
    
    Parsed with column specification:
    cols()
    Error in .subset2(x, i) : subscript out of bounds
    Calls: get_metadata ... getGEO -> parseGEO -> parseGSEMatrix -> [[ -> [[.tbl_df
    Execution halted
Flavor: r-release-linux-x86_64

Version: 1.0.1
Check: package dependencies
Result: ERROR
    Packages required but not available:
     ‘tximport’ ‘EnsDb.Hsapiens.v86’ ‘EnsDb.Rnorvegicus.v79’
     ‘EnsDb.Mmusculus.v79’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘GenomicFeatures’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Version: 1.0.1
Check: package dependencies
Result: ERROR
    Packages required but not available:
     'EnsDb.Hsapiens.v86' 'EnsDb.Mmusculus.v79' 'org.Rn.eg.db'
    
    See section 'The DESCRIPTION file' in the 'Writing R Extensions'
    manual.
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.0.1
Check: package dependencies
Result: ERROR
    Packages required but not available:
     ‘tximport’ ‘EnsDb.Hsapiens.v86’ ‘EnsDb.Rnorvegicus.v79’
     ‘EnsDb.Mmusculus.v79’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-oldrel-osx-x86_64