This page was generated on 2024-05-07 11:32:41 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup"
| 4461 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
| polyester 1.40.0 (landing page) Jack Fu , Jeff Leek
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
git_url: https://git.bioconductor.org/packages/polyester |
git_branch: RELEASE_3_19 |
git_last_commit: c0fe46d |
git_last_commit_date: 2024-04-30 10:39:11 -0400 (Tue, 30 Apr 2024) |
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | | |
CHECK results for polyester on kjohnson3
To the developers/maintainers of the polyester package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
|
raw results
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:polyester.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings polyester_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/polyester.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘polyester/DESCRIPTION’ ... OK
* this is package ‘polyester’ version ‘1.40.0’
* 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 ‘polyester’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 code 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 ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zlibbioc’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add_platform_error: no visible binding for global variable ‘model1’
add_platform_error: no visible binding for global variable ‘model2’
add_platform_error: no visible binding for global variable ‘model4’
add_platform_error: no visible binding for global variable ‘model5’
add_platform_error: no visible binding for global variable ‘model3’
add_platform_error: no visible binding for global variable ‘model6’
add_platform_error: no visible binding for global variable ‘model7’
generate_fragments: no visible binding for global variable
‘empirical_density’
generate_fragments: no visible binding for global variable ‘rnaf’
generate_fragments: no visible binding for global variable ‘cdnaf’
simulate_experiment_countmat: no visible global function definition for
‘is’
Undefined global functions or variables:
cdnaf empirical_density is model1 model2 model3 model4 model5 model6
model7 rnaf
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘polyester-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_error
> ### Title: add sequencing error to simulated reads
> ### Aliases: add_error
>
> ### ** Examples
>
> library(Biostrings)
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’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
> data(srPhiX174)
Warning in data(srPhiX174) : data set ‘srPhiX174’ not found
> set.seed(174)
> srPhiX174_withError = add_error(srPhiX174)
Error: object 'srPhiX174' not found
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/polyester.Rcheck/00check.log’
for details.
Installation output
polyester.Rcheck/00install.out
Tests output
Example timings
polyester.Rcheck/polyester-Ex.timings