CRAN Package Check Results for Package MetaSubtract

Last updated on 2018-06-29 15:49:50 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.41 1.55 20.07 21.62 ERROR
r-devel-linux-x86_64-debian-gcc 1.41 1.48 15.60 17.08 ERROR
r-devel-linux-x86_64-fedora-clang 1.41 27.09 OK
r-devel-linux-x86_64-fedora-gcc 1.41 25.78 OK
r-devel-windows-ix86+x86_64 1.41 5.00 33.00 38.00 OK
r-patched-linux-x86_64 1.41 ERROR
r-patched-solaris-x86 1.41 35.30 OK
r-release-linux-x86_64 1.41 1.94 18.52 20.46 ERROR
r-release-windows-ix86+x86_64 1.41 7.00 49.00 56.00 OK
r-release-osx-x86_64 1.41 OK
r-oldrel-windows-ix86+x86_64 1.41 5.00 43.00 48.00 OK
r-oldrel-osx-x86_64 1.3 OK

Check Details

Version: 1.41
Check: examples
Result: ERROR
    Running examples in ‘MetaSubtract-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: meta.subtract
    > ### Title: Subtracts GWAS results from one or more cohorts from the
    > ### meta-GWAS results
    > ### Aliases: meta.subtract
    > ### Keywords: Correct meta-GWAS results Leave-one-out
    >
    > ### ** Examples
    >
    > metafile="meta_results.txt"
    > cohortfiles=c("cohort1_results.txt","cohort2_results.txt","cohort3_results.txt")
    > # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
    > # Genomic control correction of the imported meta summary statistics will be undone using
    > # lambda.meta. Genomic control will be applied to the corrected meta summary statistics
    > # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics
    > # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first
    > # corrected for genomic control before subtracting them from the meta summary statistics. By
    > # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
    > m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, dir=tempdir())
    Analysis started Fri Jun 29 05:53:05 2018
    Reading /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/MetaSubtract/extdata/meta_results.txt
    Subtracting effects of /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt
     - Number of genetic markers removed because of mismatch in alleles: 1 (0.12%)
    Warning in file(file, ifelse(append, "a", "w")) :
     cannot open file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt.allele_mismatch.txt': Read-only file system
    Error in file(file, ifelse(append, "a", "w")) :
     cannot open the connection
    Calls: meta.subtract -> write.table -> file
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.41
Check: examples
Result: ERROR
    Running examples in ‘MetaSubtract-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: meta.subtract
    > ### Title: Subtracts GWAS results from one or more cohorts from the
    > ### meta-GWAS results
    > ### Aliases: meta.subtract
    > ### Keywords: Correct meta-GWAS results Leave-one-out
    >
    > ### ** Examples
    >
    > metafile="meta_results.txt"
    > cohortfiles=c("cohort1_results.txt","cohort2_results.txt","cohort3_results.txt")
    > # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
    > # Genomic control correction of the imported meta summary statistics will be undone using
    > # lambda.meta. Genomic control will be applied to the corrected meta summary statistics
    > # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics
    > # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first
    > # corrected for genomic control before subtracting them from the meta summary statistics. By
    > # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
    > m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, dir=tempdir())
    Analysis started Fri Jun 29 05:03:36 2018
    Reading /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MetaSubtract/extdata/meta_results.txt
    Subtracting effects of /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt
     - Number of genetic markers removed because of mismatch in alleles: 1 (0.12%)
    Warning in file(file, ifelse(append, "a", "w")) :
     cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt.allele_mismatch.txt': Read-only file system
    Error in file(file, ifelse(append, "a", "w")) :
     cannot open the connection
    Calls: meta.subtract -> write.table -> file
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.41
Check: examples
Result: ERROR
    Running examples in ‘MetaSubtract-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: meta.subtract
    > ### Title: Subtracts GWAS results from one or more cohorts from the
    > ### meta-GWAS results
    > ### Aliases: meta.subtract
    > ### Keywords: Correct meta-GWAS results Leave-one-out
    >
    > ### ** Examples
    >
    > metafile="meta_results.txt"
    > cohortfiles=c("cohort1_results.txt","cohort2_results.txt","cohort3_results.txt")
    > # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
    > # Genomic control correction of the imported meta summary statistics will be undone using
    > # lambda.meta. Genomic control will be applied to the corrected meta summary statistics
    > # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics
    > # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first
    > # corrected for genomic control before subtracting them from the meta summary statistics. By
    > # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
    > m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, dir=tempdir())
    Analysis started Thu Jun 28 05:50:05 2018
    Reading /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MetaSubtract/extdata/meta_results.txt
    Subtracting effects of /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt
     - Number of genetic markers removed because of mismatch in alleles: 1 (0.12%)
    Warning in file(file, ifelse(append, "a", "w")) :
     cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt.allele_mismatch.txt': Read-only file system
    Error in file(file, ifelse(append, "a", "w")) :
     cannot open the connection
    Calls: meta.subtract -> write.table -> file
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 1.41
Check: examples
Result: ERROR
    Running examples in ‘MetaSubtract-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: meta.subtract
    > ### Title: Subtracts GWAS results from one or more cohorts from the
    > ### meta-GWAS results
    > ### Aliases: meta.subtract
    > ### Keywords: Correct meta-GWAS results Leave-one-out
    >
    > ### ** Examples
    >
    > metafile="meta_results.txt"
    > cohortfiles=c("cohort1_results.txt","cohort2_results.txt","cohort3_results.txt")
    > # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
    > # Genomic control correction of the imported meta summary statistics will be undone using
    > # lambda.meta. Genomic control will be applied to the corrected meta summary statistics
    > # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics
    > # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first
    > # corrected for genomic control before subtracting them from the meta summary statistics. By
    > # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
    > m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, dir=tempdir())
    Analysis started Thu Jun 28 17:48:21 2018
    Reading /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/MetaSubtract/extdata/meta_results.txt
    Subtracting effects of /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt
     - Number of genetic markers removed because of mismatch in alleles: 1 (0.12%)
    Warning in file(file, ifelse(append, "a", "w")) :
     cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/MetaSubtract/extdata/cohort1_results.txt.allele_mismatch.txt': Read-only file system
    Error in file(file, ifelse(append, "a", "w")) :
     cannot open the connection
    Calls: meta.subtract -> write.table -> file
    Execution halted
Flavor: r-release-linux-x86_64