CRAN Package Check Results for Package SynergizeR

Last updated on 2018-05-03 10:51:33 CEST.

Check Details

Version: 0.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SynergizeR.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Title field: should not end in a period.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘RCurl’ ‘RJSONIO’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2
Check: R code for possible problems
Result: NOTE
    File ‘SynergizeR/R/zzz.r’:
     .onLoad calls:
     packageStartupMessage("\nSynergizeR\n", appendLF = TRUE)
     packageStartupMessage("IMPORTANT: The Synergizer has been designed for bulk translation of identifiers.\nSee http://llama.mshri.on.ca/synergizer/doc/ for the details of usage. ", appendLF = TRUE)
    
    See section ‘Good practice’ in '?.onAttach'.
    
    available_authorities: no visible global function definition for
     ‘getCurlHandle’
    available_authorities: no visible global function definition for
     ‘curlSetOpt’
    available_authorities: no visible global function definition for
     ‘basicTextGatherer’
    available_authorities: no visible global function definition for
     ‘basicHeaderGatherer’
    available_authorities: no visible global function definition for
     ‘curlPerform’
    available_authorities: no visible global function definition for
     ‘fromJSON’
    available_domains: no visible global function definition for
     ‘getCurlHandle’
    available_domains: no visible global function definition for
     ‘curlSetOpt’
    available_domains: no visible global function definition for
     ‘basicTextGatherer’
    available_domains: no visible global function definition for
     ‘basicHeaderGatherer’
    available_domains: no visible global function definition for
     ‘curlPerform’
    available_domains: no visible global function definition for ‘fromJSON’
    available_ranges: no visible global function definition for
     ‘getCurlHandle’
    available_ranges: no visible global function definition for
     ‘curlSetOpt’
    available_ranges: no visible global function definition for
     ‘basicTextGatherer’
    available_ranges: no visible global function definition for
     ‘basicHeaderGatherer’
    available_ranges: no visible global function definition for
     ‘curlPerform’
    available_ranges: no visible global function definition for ‘fromJSON’
    available_species: no visible global function definition for
     ‘getCurlHandle’
    available_species: no visible global function definition for
     ‘curlSetOpt’
    available_species: no visible global function definition for
     ‘basicTextGatherer’
    available_species: no visible global function definition for
     ‘basicHeaderGatherer’
    available_species: no visible global function definition for
     ‘curlPerform’
    available_species: no visible global function definition for ‘fromJSON’
    server_version: no visible global function definition for
     ‘getCurlHandle’
    server_version: no visible global function definition for ‘curlSetOpt’
    server_version: no visible global function definition for
     ‘basicTextGatherer’
    server_version: no visible global function definition for
     ‘basicHeaderGatherer’
    server_version: no visible global function definition for ‘curlPerform’
    server_version: no visible global function definition for ‘fromJSON’
    synergizer: no visible global function definition for
     ‘basicTextGatherer’
    synergizer: no visible global function definition for
     ‘basicHeaderGatherer’
    synergizer: no visible global function definition for ‘curlPerform’
    synergizer: no visible global function definition for ‘getCurlHandle’
    synergizer: no visible global function definition for ‘toJSON’
    synergizer: no visible global function definition for ‘fromJSON’
    synergizer: no visible global function definition for ‘write.table’
    Undefined global functions or variables:
     basicHeaderGatherer basicTextGatherer curlPerform curlSetOpt fromJSON
     getCurlHandle toJSON write.table
    Consider adding
     importFrom("utils", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.2
Check: Rd line widths
Result: NOTE
    Rd file 'available_ranges.Rd':
     \usage lines wider than 90 characters:
     available_ranges(authority = "ensembl", species = "Homo sapiens", domain = "hgnc_symbol")
    
    Rd file 'synergizer.Rd':
     \usage lines wider than 90 characters:
     synergizer(authority = "ensembl", species = "Homo sapiens", domain = "hgnc_symbol", range = "entrezgene", ids = NULL, file = NULL)
     \examples lines wider than 100 characters:
     symbols.ids <- synergizer( authority = "ensembl", species = "Homo sapiens", domain="affy_hg_u95av2", range="hgnc_symbol",ids=c("1939_at ... [TRUNCATED]
     entrez.ids <- synergizer( authority = "ensembl", species = "Homo sapiens", domain="hgnc_symbol", range="entrezgene",ids=c("snph", "pja1 ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SynergizeR.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-clang/SynergizeR.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-devel/SynergizeR.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See 'd:/Rcompile/CRANpkg/local/3.5/SynergizeR.Rcheck/00install.out' for details.
    Information on the location(s) of code generating the 'Note's can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to 'yes'.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/SynergizeR.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-linux-x86_64

Version: 0.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/ripley/R/packages/tests32/SynergizeR.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-solaris-x86

Version: 0.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SynergizeR.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-linux-x86_64

Version: 0.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SynergizeR.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-osx-x86_64