CRAN Package Check Results for Package lmQCM

Last updated on 2020-08-07 01:49:51 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.1 18.52 165.41 183.93 ERROR
r-devel-linux-x86_64-debian-gcc 0.2.1 16.19 125.92 142.11 ERROR
r-devel-linux-x86_64-fedora-clang 0.2.1 227.40 ERROR
r-devel-linux-x86_64-fedora-gcc 0.2.1 218.48 ERROR
r-devel-windows-ix86+x86_64 0.2.1 49.00 165.00 214.00 ERROR
r-patched-linux-x86_64 0.2.1 19.84 160.21 180.05 OK
r-patched-solaris-x86 0.2.1 328.50 OK
r-release-linux-x86_64 0.2.1 19.18 163.44 182.62 OK
r-release-macos-x86_64 0.2.1 OK
r-release-windows-ix86+x86_64 0.2.1 49.00 213.00 262.00 OK
r-oldrel-macos-x86_64 0.2.1 OK
r-oldrel-windows-ix86+x86_64 0.2.1 34.00 200.00 234.00 OK

Check Details

Version: 0.2.1
Check: examples
Result: ERROR
    Running examples in 'lmQCM-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: lmQCM
    > ### Title: lmQCM: Main Routine for Gene Co-expression Analysis
    > ### Aliases: lmQCM
    >
    > ### ** Examples
    >
    > library(lmQCM)
    > library(Biobase)
    > data(sample.ExpressionSet)
    > data = assayData(sample.ExpressionSet)$exprs
    > data = fastFilter(data, 0.2, 0.2)
    Note: For RNA data, we suppose input matrix (data frame) is with:
     Row: Genes; Columns: Samples.
    (400 genes, 26 samples) after removing lowest 20.00% mean expression value.
    Calculating the variances.
    (320 genes, 26 samples) after removing lowest 20.00% variance expression value.
    > lmQCM(data)
    Calculating massive correlation coefficient ...
    Number of Maximum Edges: 114
     Calculation Finished.
     48 Modules before merging.
     4 Modules remain after merging.
    Error in svd(XNorm, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
    Calls: lmQCM -> svd
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.2.1
Check: tests
Result: ERROR
     Running 'run_test_lmQCM.R' [8s/9s]
    Running the tests in 'tests/run_test_lmQCM.R' failed.
    Complete output:
     > library(lmQCM)
     Loading required package: genefilter
     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, 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")'.
    
     Loading required package: progress
     Package lmQCM 0.2.1 loaded.
    
     ==========================================================================
    
     If you benefit from this package, please cite:
    
     Zhang, Jie & Huang, Kun (2014)
     Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques
     in Weighted Graph with Applications in Gene Co-Expression Module
     Discovery in Cancers. Cancer informatics, 13, CIN-S14021.
    
     ==========================================================================
    
    
     > library(Biobase)
     > data(sample.ExpressionSet)
     > data = assayData(sample.ExpressionSet)$exprs
     > lmQCM(data)
     Calculating massive correlation coefficient ...
     Number of Maximum Edges: 154
     Calculation Finished.
     64 Modules before merging.
     5 Modules remain after merging.
     Error in svd(XNorm, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: lmQCM -> svd
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.1
Check: tests
Result: ERROR
     Running ‘run_test_lmQCM.R’ [6s/9s]
    Running the tests in ‘tests/run_test_lmQCM.R’ failed.
    Complete output:
     > library(lmQCM)
     Loading required package: genefilter
     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, 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")'.
    
     Loading required package: progress
     Package lmQCM 0.2.1 loaded.
    
     ==========================================================================
    
     If you benefit from this package, please cite:
    
     Zhang, Jie & Huang, Kun (2014)
     Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques
     in Weighted Graph with Applications in Gene Co-Expression Module
     Discovery in Cancers. Cancer informatics, 13, CIN-S14021.
    
     ==========================================================================
    
    
     > library(Biobase)
     > data(sample.ExpressionSet)
     > data = assayData(sample.ExpressionSet)$exprs
     > lmQCM(data)
     Calculating massive correlation coefficient ...
     Number of Maximum Edges: 154
     Calculation Finished.
     64 Modules before merging.
     5 Modules remain after merging.
     Error in svd(XNorm, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: lmQCM -> svd
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.1
Check: examples
Result: ERROR
    Running examples in ‘lmQCM-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: lmQCM
    > ### Title: lmQCM: Main Routine for Gene Co-expression Analysis
    > ### Aliases: lmQCM
    >
    > ### ** Examples
    >
    > library(lmQCM)
    > library(Biobase)
    > data(sample.ExpressionSet)
    > data = assayData(sample.ExpressionSet)$exprs
    > data = fastFilter(data, 0.2, 0.2)
    Note: For RNA data, we suppose input matrix (data frame) is with:
     Row: Genes; Columns: Samples.
    (400 genes, 26 samples) after removing lowest 20.00% mean expression value.
    Calculating the variances.
    (320 genes, 26 samples) after removing lowest 20.00% variance expression value.
    > lmQCM(data)
    Calculating massive correlation coefficient ...
    Number of Maximum Edges: 114
     Calculation Finished.
     48 Modules before merging.
     4 Modules remain after merging.
    Error in svd(XNorm, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
    Calls: lmQCM -> svd
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 0.2.1
Check: tests
Result: ERROR
     Running ‘run_test_lmQCM.R’ [9s/11s]
    Running the tests in ‘tests/run_test_lmQCM.R’ failed.
    Complete output:
     > library(lmQCM)
     Loading required package: genefilter
     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, 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")'.
    
     Loading required package: progress
     Package lmQCM 0.2.1 loaded.
    
     ==========================================================================
    
     If you benefit from this package, please cite:
    
     Zhang, Jie & Huang, Kun (2014)
     Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques
     in Weighted Graph with Applications in Gene Co-Expression Module
     Discovery in Cancers. Cancer informatics, 13, CIN-S14021.
    
     ==========================================================================
    
    
     > library(Biobase)
     > data(sample.ExpressionSet)
     > data = assayData(sample.ExpressionSet)$exprs
     > lmQCM(data)
     Calculating massive correlation coefficient ...
     Number of Maximum Edges: 154
     Calculation Finished.
     64 Modules before merging.
     5 Modules remain after merging.
     Error in svd(XNorm, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: lmQCM -> svd
     Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.2.1
Check: tests
Result: ERROR
     Running 'run_test_lmQCM.R' [7s]
    Running the tests in 'tests/run_test_lmQCM.R' failed.
    Complete output:
     > library(lmQCM)
     Loading required package: genefilter
     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, 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")'.
    
     Loading required package: progress
     Package lmQCM 0.2.1 loaded.
    
     ==========================================================================
    
     If you benefit from this package, please cite:
    
     Zhang, Jie & Huang, Kun (2014)
     Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques
     in Weighted Graph with Applications in Gene Co-Expression Module
     Discovery in Cancers. Cancer informatics, 13, CIN-S14021.
    
     ==========================================================================
    
    
     > library(Biobase)
     > data(sample.ExpressionSet)
     > data = assayData(sample.ExpressionSet)$exprs
     > lmQCM(data)
     Calculating massive correlation coefficient ...
     Number of Maximum Edges: 154
     Calculation Finished.
     64 Modules before merging.
     5 Modules remain after merging.
     Error in svd(XNorm, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: lmQCM -> svd
     Execution halted
Flavor: r-devel-windows-ix86+x86_64