nebbiolo1 Summary
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Package: IntOMICS |
Version: 0.99.8 |
RVersion: 4.3
|
BiocVersion: 3.17
|
BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data IntOMICS |
BuildTime: 1 minutes 27.90 seconds |
CheckCommand: BiocCheckGitClone('IntOMICS') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2744/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS.install-out.txt IntOMICS_0.99.8.tar.gz && BiocCheck('IntOMICS_0.99.8.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 20.27 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 2561.67 KiB |
BuildID:: IntOMICS_20221202155022 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: IntOMICS. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘IntOMICS/DESCRIPTION’ ... OK
* preparing ‘IntOMICS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘IntOMICS_0.99.8.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('IntOMICS')
===============================
─ BiocCheckVersion: 1.35.4
─ BiocVersion: 3.17
─ Package: IntOMICS
─ PackageVersion: 0.99.8
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntOMICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IntOMICS’ version ‘0.99.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IntOMICS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [28s/28s] NOTE
dens_edge_weights: no visible binding for global variable ‘edge_weight’
dens_edge_weights: no visible binding for global variable ‘scaled’
ggraph_weighted_net: no visible binding for global variable
‘weighted_net_res’
ggraph_weighted_net: no visible binding for global variable
‘node2.degree’
ggraph_weighted_net: no visible binding for global variable ‘weight’
ggraph_weighted_net: no visible binding for global variable ‘color’
ggraph_weighted_net: no visible binding for global variable ‘label’
legend_custom_ggplot: no visible binding for global variable ‘x_min’
legend_custom_ggplot: no visible binding for global variable ‘x_max’
legend_custom_ggplot: no visible binding for global variable ‘y_min’
legend_custom_ggplot: no visible binding for global variable ‘y_max’
legend_custom_ggplot: no visible binding for global variable ‘x_lab’
legend_custom_ggplot: no visible binding for global variable ‘val’
Undefined global functions or variables:
color edge_weight label node2.degree scaled val weight
weighted_net_res x_lab x_max x_min y_max y_min
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [12s/12s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] ERROR
Running examples in ‘IntOMICS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: b_prior_mat
> ### Title: biological prior matrix
> ### Aliases: b_prior_mat
> ### Keywords: internal
>
> ### ** Examples
>
> data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics", "gene_annot"),
+ package="IntOMICS")
> omics <- omics_to_list(omics = omics, gene_annot = gene_annot,
+ layers_def = layers_def)
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
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
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
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: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': file '/home/annapacinkova/.cache/R/ExperimentHub/4a8d7c2fdea_4873' does not exist
Calls: omics_to_list ... h5getdimscales -> .Call2 -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/13s]
[13s/13s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
11. │ ├─BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
12. │ └─base::lapply(as.list(X), match.fun(FUN), ...)
13. │ └─SummarizedExperiment (local) FUN(X[[i]], ...)
14. │ ├─methods (local) dimnames(a)
15. │ └─DelayedArray (local) dimnames(a)
16. │ ├─methods::callNextMethod()
17. │ └─DelayedArray (local) .nextMethod(x = x)
18. │ ├─methods (local) dimnames(x@seed)
19. │ └─DelayedArray (local) dimnames(x@seed)
20. │ ├─DelayedArray:::subset_dimnames_by_Nindex(dimnames(x@seed), x@index)
21. │ ├─methods (local) dimnames(x@seed)
22. │ └─HDF5Array (local) dimnames(x@seed)
23. │ └─HDF5Array::h5readDimnames(x@filepath, x@name, as.character = TRUE)
24. │ └─HDF5Array::get_h5dimnames(filepath, name)
25. │ └─HDF5Array:::h5getdimscales(filepath, name, scalename = "dimnames")
26. │ └─S4Vectors::.Call2(...)
27. └─base::.handleSimpleError(...)
28. └─base (local) h(simpleError(msg, call))
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 11 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS.Rcheck/00check.log’
for details.
===============================
BiocCheck('IntOMICS_0.99.8.tar.gz')
===============================
─ BiocCheckVersion: 1.35.4
─ BiocVersion: 3.17
─ Package: IntOMICS
─ PackageVersion: 0.99.8
─ sourceDir: /tmp/RtmpVQFBVN/file31dc6576c19568/IntOMICS
─ installDir: /tmp/RtmpVQFBVN/file31dc65702e056f
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of IntOMICS...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/dens_edge_weights.Rd
Found @ in man/ggraph_weighted_net.Rd
Found @ in man/legend_custom_ggplot.Rd
Found @ in man/weighted_net.Rd
Found @ in vignettes/IntOMICS_vignette.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 132 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 97 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 815 lines
(11%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* NOTE: Cannot determine whether maintainer is subscribed to the
Bioc-Devel mailing list (requires admin credentials). Subscribe
here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 9 NOTES
See the IntOMICS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
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Package: IntOMICS |
Version: 0.99.8 |
RVersion: 4.3
|
BiocVersion: 3.17
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data IntOMICS |
BuildTime: 1 minutes 39.01 seconds |
CheckCommand: BiocCheckGitClone('IntOMICS') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2744/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS.install-out.txt IntOMICS_0.99.8.tar.gz && BiocCheck('IntOMICS_0.99.8.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 52.40 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh IntOMICS_0.99.8.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 28.80 seconds |
PackageFileSize: 2555.41 KiB |
BuildID:: IntOMICS_20221202155022 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: IntOMICS. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘IntOMICS/DESCRIPTION’ ... OK
* preparing ‘IntOMICS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘IntOMICS_0.99.8.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('IntOMICS')
===============================
─ BiocCheckVersion: 1.35.4
─ BiocVersion: 3.17
─ Package: IntOMICS
─ PackageVersion: 0.99.8
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntOMICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IntOMICS’ version ‘0.99.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IntOMICS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [32s/32s] NOTE
dens_edge_weights: no visible binding for global variable ‘edge_weight’
dens_edge_weights: no visible binding for global variable ‘scaled’
ggraph_weighted_net: no visible binding for global variable
‘weighted_net_res’
ggraph_weighted_net: no visible binding for global variable
‘node2.degree’
ggraph_weighted_net: no visible binding for global variable ‘weight’
ggraph_weighted_net: no visible binding for global variable ‘color’
ggraph_weighted_net: no visible binding for global variable ‘label’
legend_custom_ggplot: no visible binding for global variable ‘x_min’
legend_custom_ggplot: no visible binding for global variable ‘x_max’
legend_custom_ggplot: no visible binding for global variable ‘y_min’
legend_custom_ggplot: no visible binding for global variable ‘y_max’
legend_custom_ggplot: no visible binding for global variable ‘x_lab’
legend_custom_ggplot: no visible binding for global variable ‘val’
Undefined global functions or variables:
color edge_weight label node2.degree scaled val weight
weighted_net_res x_lab x_max x_min y_max y_min
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [14s/14s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] ERROR
Running examples in ‘IntOMICS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: b_prior_mat
> ### Title: biological prior matrix
> ### Aliases: b_prior_mat
> ### Keywords: internal
>
> ### ** Examples
>
> data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics", "gene_annot"),
+ package="IntOMICS")
> omics <- omics_to_list(omics = omics, gene_annot = gene_annot,
+ layers_def = layers_def)
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
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
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
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: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': file '/home/annapacinkova/.cache/R/ExperimentHub/4a8d7c2fdea_4873' does not exist
Calls: omics_to_list ... h5getdimscales -> .Call2 -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [14s/14s]
[14s/14s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
11. │ ├─BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
12. │ └─base::lapply(as.list(X), match.fun(FUN), ...)
13. │ └─SummarizedExperiment (local) FUN(X[[i]], ...)
14. │ ├─methods (local) dimnames(a)
15. │ └─DelayedArray (local) dimnames(a)
16. │ ├─methods::callNextMethod()
17. │ └─DelayedArray (local) .nextMethod(x = x)
18. │ ├─methods (local) dimnames(x@seed)
19. │ └─DelayedArray (local) dimnames(x@seed)
20. │ ├─DelayedArray:::subset_dimnames_by_Nindex(dimnames(x@seed), x@index)
21. │ ├─methods (local) dimnames(x@seed)
22. │ └─HDF5Array (local) dimnames(x@seed)
23. │ └─HDF5Array::h5readDimnames(x@filepath, x@name, as.character = TRUE)
24. │ └─HDF5Array::get_h5dimnames(filepath, name)
25. │ └─HDF5Array:::h5getdimscales(filepath, name, scalename = "dimnames")
26. │ └─S4Vectors::.Call2(...)
27. └─base::.handleSimpleError(...)
28. └─base (local) h(simpleError(msg, call))
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 11 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [5s/6s] OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS.Rcheck/00check.log’
for details.
===============================
BiocCheck('IntOMICS_0.99.8.tar.gz')
===============================
─ BiocCheckVersion: 1.35.4
─ BiocVersion: 3.17
─ Package: IntOMICS
─ PackageVersion: 0.99.8
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp97kF1S/file621c2fcfac19/IntOMICS
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp97kF1S/file621c2aea844
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2744/b38c7b3652dab4655486ad4935fb3aa60d3e08cd/IntOMICS.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of IntOMICS...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/dens_edge_weights.Rd
Found @ in man/ggraph_weighted_net.Rd
Found @ in man/legend_custom_ggplot.Rd
Found @ in man/weighted_net.Rd
Found @ in vignettes/IntOMICS_vignette.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 132 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 97 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 815 lines
(11%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* NOTE: Cannot determine whether maintainer is subscribed to the
Bioc-Devel mailing list (requires admin credentials). Subscribe
here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 9 NOTES
See the IntOMICS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir IntOMICS_0.99.8.tar.gz'
>>>>>>>
* installing *source* package ‘IntOMICS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IntOMICS)