===============================
BiocCheckGitClone('MotifPeeker')
===============================
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3483/MotifPeeker_20240809145815/MotifPeeker
─ BiocVersion: 3.20
─ Package: MotifPeeker
─ PackageVersion: 0.99.1
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3483/MotifPeeker_20240809145815/MotifPeeker.BiocCheck
─ BiocCheckVersion: 1.41.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3483/MotifPeeker_20240809145815/MotifPeeker
─ installDir: NULL
─ isTarBall: FALSE
─ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3483/MotifPeeker_20240809145815/MotifPeeker.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MotifPeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MotifPeeker’ version ‘0.99.1’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MotifPeeker’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: there is no package called ‘zlibbioc’
Call sequence:
13: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
11: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
10: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
9: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
8: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = packa
Execution halted
* checking S3 generic/method consistency ... WARNING
Error: there is no package called ‘zlibbioc’
Call sequence:
13: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
11: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
10: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
9: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
8: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = packa
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error: there is no package called ‘zlibbioc’
Call sequence:
13: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
11: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
10: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
9: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
8: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = packa
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: there is no package called ‘zlibbioc’
Call sequence:
13: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
11: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
10: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
9: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
8: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = packa
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [18s/19s] NOTE
Error: there is no package called ‘Biobase’
Call sequence:
19: doWithOneRestart(return(expr), restart)
18: withOneRestart(expr, restarts[[1L]])
17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
16: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
15: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
14: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
13: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
12: loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
11: asNamespace(ns)
10: asNamespace(ns)
9: namespaceImportFrom(self, asNamespace(ns), vars, from = from)
8: namespaceImportClasses(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), imp[[2L]], from = package)
7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
Execution halted
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘BiocGenerics’
Calls: <Anonymous>
Execution halted
* checking Rd files ... [0s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Error: package or namespace load failed for ‘MotifPeeker’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘Biobase’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return && !quietly)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc, character
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 ... 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 ... [3s/4s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [174s/109s] ERROR
Running examples in ‘MotifPeeker-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MotifPeeker
> ### Title: Benchmark epigenomic profiling methods using motif enrichment
> ### Aliases: MotifPeeker
>
> ### ** Examples
>
> peaks <- list(
+ system.file("extdata", "CTCF_ChIP_peaks.narrowPeak",
+ package = "MotifPeeker"),
+ system.file("extdata", "CTCF_TIP_peaks.narrowPeak",
+ package = "MotifPeeker")
+ )
>
> alignments <- list(
+ system.file("extdata", "CTCF_ChIP_alignment.bam",
+ package = "MotifPeeker"),
+ system.file("extdata", "CTCF_TIP_alignment.bam",
+ package = "MotifPeeker")
+ )
>
> motifs <- list(
+ system.file("extdata", "motif_MA1930.2.jaspar",
+ package = "MotifPeeker"),
+ system.file("extdata", "motif_MA1102.3.jaspar",
+ package = "MotifPeeker")
+ )
>
> MotifPeeker(
+ peak_files = peaks,
+ reference_index = 1,
+ alignment_files = alignments,
+ exp_labels = c("ChIP", "TIP"),
+ exp_type = c("chipseq", "tipseq"),
+ genome_build = "hg38",
+ motif_files = motifs,
+ motif_labels = NULL,
+ cell_counts = NULL,
+ denovo_motif_discovery = TRUE,
+ denovo_motifs = 3,
+ motif_db = NULL,
+ download_buttons = TRUE,
+ out_dir = tempdir(),
+ workers = 2,
+ debug = FALSE,
+ quiet = TRUE,
+ verbose = FALSE
+ )
Error in `x[["Version"]]`:
! subscript out of bounds
Backtrace:
1. rmarkdown::render(...)
2. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
3. knitr:::process_file(text, output)
6. knitr:::process_group(group)
7. knitr:::call_block(x)
...
25. utils:::print.sessionInfo(x)
27. utils (local) mkLabel(x, "loadedOnly")
28. base::sapply(L[[n]], function(x) x[["Version"]])
29. base::lapply(X = X, FUN = FUN, ...)
30. utils (local) FUN(X[[i]], ...)
Quitting from lines 925-926 [Session Info] (MotifPeeker.Rmd)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[2s/2s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> desc_path <- list.files("../","^DESCRIPTION$",
+ full.names = TRUE, recursive = TRUE)[1]
> pkg <- read.dcf(desc_path, fields = "Package")[1]
> library(testthat)
> library(pkg, character.only = TRUE)
Error: package or namespace load failed for 'MotifPeeker' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called 'IRanges'
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 ... [7s/10s] OK
* DONE
Status: 2 ERRORs, 3 WARNINGs, 4 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3483/MotifPeeker_20240809145815/MotifPeeker.Rcheck/00check.log’
for details.
===============================
BiocCheck('MotifPeeker_0.99.1.tar.gz')
===============================
Error: package or namespace load failed for ‘BiocCheck’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘RBGL’
Execution halted