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 |
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