===============================
BiocCheckGitClone('DeepTarget')
===============================
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: DeepTarget
─ PackageVersion: 0.99.9
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3066/900376fd6fa949b4287b48e8363db4ac9a9f5e98/DeepTarget
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ 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/3066/900376fd6fa949b4287b48e8363db4ac9a9f5e98/DeepTarget.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeepTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepTarget’ version ‘0.99.9’
* 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 ‘DeepTarget’ 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] WARNING
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘ComplexHeatmap’
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 ... [2s/2s] WARNING
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘ComplexHeatmap’
Calls: suppressMessages ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking loading without being on the library search path ... [2s/2s] WARNING
Error: package or namespace load failed for ‘DeepTarget’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘ComplexHeatmap’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: there is no package called ‘ComplexHeatmap’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
5: asNamespace(ns)
4: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
Execution halted
* checking S3 generic/method consistency ... WARNING
Error: there is no package called ‘ComplexHeatmap’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
5: asNamespace(ns)
4: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s/10s] NOTE
Error: there is no package called ‘DEGreport’
Call sequence:
6: doWithOneRestart(return(expr), restart)
5: withOneRestart(expr, restarts[[1L]])
4: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
Execution halted
Error in namespaceExport(ns, exports) :
undefined exports: DEGSet, as.DEGSet, createReport, deg, degCheckFactors, degColors, degComps, degCorCov, degCorrect, degCovariates, degDefault, degFilter, degMA, degMB, degMDS, degMV, degMean, degObj, degPCA, degPatterns, degPlot, degPlotCluster, degPlotWide, degQC, degResults, degSignature, degSummary, degVB, degVar, degVolcano, geom_cor, significants
Calls: <Anonymous>
Execution halted
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'colorBar.Rd':
\examples lines wider than 100 characters:
plot(x, y, pch = 19, col = y.clr , xlab="-log10(Pval)", ylab= paste0("correlation strength ",colnames(Pval)[1]));
Rd file 'cor.test_trimmed_v0.default.Rd':
\usage lines wider than 90 characters:
cor.test_trimmed_v0.default(x, y, alternative = c("two.sided", "less", "greater"), method = c("pearson"), exact = NULL, continuity = FA ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Error: package or namespace load failed for ‘DeepTarget’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘DEGreport’
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, characte
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 or namespace load failed for ‘DeepTarget’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘DEGreport’
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, characte
Execution halted
Error: package or namespace load failed for ‘DeepTarget’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘DEGreport’
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, characte
Execution halted
Error: package or namespace load failed for ‘DeepTarget’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘DEGreport’
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, characte
Execution halted
* checking Rd \usage sections ... NOTE
Error: there is no package called ‘DEGreport’
Call sequence:
6: doWithOneRestart(return(expr), restart)
5: withOneRestart(expr, restarts[[1L]])
4: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/0s] ERROR
Running examples in ‘DeepTarget-Ex.R’ failed
The error occurred in:
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 <- "DeepTarget"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> base::assign(".ExTimings", "DeepTarget-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('DeepTarget')
Error: package or namespace load failed for ‘DeepTarget’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘DEGreport’
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: 1 ERROR, 6 WARNINGs, 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3066/900376fd6fa949b4287b48e8363db4ac9a9f5e98/DeepTarget.Rcheck/00check.log’
for details.
===============================
BiocCheck('DeepTarget_0.99.9.tar.gz')
===============================
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3066/900376fd6fa949b4287b48e8363db4ac9a9f5e98/DeepTarget_0.99.9.tar.gz
must be installable.
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3066/900376fd6fa949b4287b48e8363db4ac9a9f5e98/DeepTarget_0.99.9.tar.gz
must be loadable.
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: DeepTarget
─ PackageVersion: 0.99.9
─ sourceDir: /tmp/RtmpJVHIvq/file38a737391aeb42/DeepTarget
─ installDir: /tmp/RtmpJVHIvq/file38a7371aabc851
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3066/900376fd6fa949b4287b48e8363db4ac9a9f5e98/DeepTarget.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 3.5.0 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...
* NOTE: Consider adding these automatically suggested biocViews:
CRISPR
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* 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 recommeded fields in DESCRIPTION...
* NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
no package 'DeepTarget' was found
Error in pkg_desc$Imports : $ operator is invalid for atomic vectors
Calls: BiocCheck ... checkDescriptionNamespaceConsistency -> cleanupDependency
Execution halted