===============================
BiocCheckGitClone('VectraPolarisData')
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This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
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R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2594/27e1a49709b20ae7094b05377a0bda96bd64cdce/VectraPolarisData.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VectraPolarisData/DESCRIPTION’ ... OK
* this is package ‘VectraPolarisData’ version ‘0.99.4’
* 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 serialization versions ... OK
* checking whether package ‘VectraPolarisData’ can be installed ... [40s/40s] 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 ... OK
* checking whether the package can be loaded with stated dependencies ...Loading required package: ExperimentHub
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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, 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: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: SpatialExperiment
Loading required package: SingleCellExperiment
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: 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
The following object is masked from ‘package:ExperimentHub’:
cache
The following object is masked from ‘package:AnnotationHub’:
cache
Error: package or namespace load failed for ‘SpatialExperiment’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘limma’
Error: package ‘SpatialExperiment’ could not be loaded
Execution halted
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package. All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* checking whether the package can be unloaded cleanly ... WARNING
Error: package ‘SpatialExperiment’ could not be loaded
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘limma’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
Error: package ‘SpatialExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error: package ‘SpatialExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [32s/32s] NOTE
Error: package ‘SpatialExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘edgeR’
Calls: <Anonymous>
Execution halted
* 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 ... WARNING
Error: package ‘SpatialExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Error: package ‘SpatialExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package ‘SpatialExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package ‘SpatialExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
* checking Rd \usage sections ... NOTE
Error: package ‘SpatialExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] ERROR
Running examples in ‘VectraPolarisData-Ex.R’ failed
The error occurred in:
R Under development (unstable) (2022-03-17 r81925) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> pkgname <- "VectraPolarisData"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> base::assign(".ExTimings", "VectraPolarisData-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+ options(OutDec = '.')
+ format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
>
> ### * </HEADER>
> library('VectraPolarisData')
Loading required package: ExperimentHub
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, 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: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: SpatialExperiment
Loading required package: SingleCellExperiment
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: 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
The following object is masked from ‘package:ExperimentHub’:
cache
The following object is masked from ‘package:AnnotationHub’:
cache
Error: package or namespace load failed for ‘SpatialExperiment’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘Rhdf5lib’
Error: package ‘SpatialExperiment’ could not be loaded
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 ... OK
* DONE
Status: 1 ERROR, 5 WARNINGs, 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2594/27e1a49709b20ae7094b05377a0bda96bd64cdce/VectraPolarisData.Rcheck/00check.log’
for details.
===============================
BiocCheck('VectraPolarisData_0.99.4.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
cmd: /Library/Frameworks/R.framework/Resources/bin/R
args: --vanilla CMD INSTALL --no-test-load --library=/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpjd1nHx/file498027c2828b/lib '/Users/pkgbuild/packagebuilder/workers/jobs/2594/27e1a49709b20ae7094b05377a0bda96bd64cdce/VectraPolarisData_0.99.4.tar.gz'
stderr:
* installing *source* package ‘VectraPolarisData’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
ERROR: lazy loading failed for package ‘VectraPolarisData’
* removing ‘/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/Rtmpjd1nHx/file498027c2828b/lib/VectraPolarisData’
* ERROR:
/Users/pkgbuild/packagebuilder/workers/jobs/2594/27e1a49709b20ae7094b05377a0bda96bd64cdce/VectraPolarisData_0.99.4.tar.gz
must be installable.
cmd: /Library/Frameworks/R.framework/Resources/bin/R
args: --vanilla -e 'library(VectraPolarisData)'
stderr:
Loading required package: ExperimentHub
Error: package ‘BiocGenerics’ required by ‘ExperimentHub’ could not be found
Execution halted
* ERROR:
/Users/pkgbuild/packagebuilder/workers/jobs/2594/27e1a49709b20ae7094b05377a0bda96bd64cdce/VectraPolarisData_0.99.4.tar.gz
must be loadable.
* Checking Package Dependencies...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
no package 'VectraPolarisData' was found
Error: $ operator is invalid for atomic vectors
Execution halted