Last updated on 2023-05-25 08:56:10 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 53.41 | 504.83 | 558.24 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 40.65 | 381.88 | 422.53 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 754.05 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 726.81 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.0 | 44.00 | 345.00 | 389.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 40.07 | 474.78 | 514.85 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 33.91 | 469.38 | 503.29 | OK | |
| r-release-macos-arm64 | 0.1.0 | 5.00 | ERROR | |||
| r-release-windows-x86_64 | 0.1.0 | 61.00 | 473.00 | 534.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | 6.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 0.1.0 | 249.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.1.0 | 58.00 | 461.00 | 519.00 | OK |
Version: 0.1.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'RCyjs', 'BrowserViz'
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-macos-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [92s/303s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(RCPA)
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:testthat':
matches
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: ggplot2
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("RCPA")
Attaching package: 'limma'
The following object is masked from 'package:RCPA':
plotMA
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object is masked from 'package:limma':
plotMA
The following object is masked from 'package:RCPA':
plotMA
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
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, aperm, 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.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:tidyr':
expand
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:dplyr':
select
Loading required package: org.Hs.eg.db
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
The following object is masked from 'package:dplyr':
count
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading 'meta' package (version 6.2-1).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs
[ FAIL 1 | WARN 4 | SKIP 71 | PASS 122 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (71)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plot-pathway-network.R:2:1'): (code run outside of `test_that()`) ──
<packageNotFoundError/error/condition>
Error in `library(RCyjs)`: there is no package called 'RCyjs'
Backtrace:
▆
1. └─base::library(RCyjs) at test-plot-pathway-network.R:2:0
[ FAIL 1 | WARN 4 | SKIP 71 | PASS 122 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [90s/447s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(RCPA)
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:testthat':
matches
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: ggplot2
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("RCPA")
Attaching package: 'limma'
The following object is masked from 'package:RCPA':
plotMA
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
converting counts to integer mode
using supplied model matrix
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object is masked from 'package:limma':
plotMA
The following object is masked from 'package:RCPA':
plotMA
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
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, aperm, 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.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:tidyr':
expand
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:dplyr':
select
Loading required package: org.Hs.eg.db
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
The following object is masked from 'package:dplyr':
count
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading 'meta' package (version 6.2-1).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs
[ FAIL 1 | WARN 4 | SKIP 71 | PASS 122 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (71)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plot-pathway-network.R:2:1'): (code run outside of `test_that()`) ──
<packageNotFoundError/error/condition>
Error in `library(RCyjs)`: there is no package called 'RCyjs'
Backtrace:
▆
1. └─base::library(RCyjs) at test-plot-pathway-network.R:2:0
[ FAIL 1 | WARN 4 | SKIP 71 | PASS 122 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘oligo’
Packages suggested but not available for checking:
'ROntoTools', 'RCyjs', 'BrowserViz', 'hgu133plus2.db'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-release-macos-arm64
Version: 0.1.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘oligo’
Packages suggested but not available for checking:
'ROntoTools', 'RCyjs', 'BrowserViz'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [28s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (71)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plot-pathway-network.R:2:1'): (code run outside of `test_that()`) ──
<packageNotFoundError/error/condition>
Error in `library(RCyjs)`: there is no package called 'RCyjs'
Backtrace:
▆
1. └─base::library(RCyjs) at test-plot-pathway-network.R:2:0
[ FAIL 1 | WARN 4 | SKIP 71 | PASS 122 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-x86_64