gCrisprTools 1.11.2
Peter Haverty
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/gCrisprTools |
| Branch: master |
| Last Commit: 46e2014 |
| Last Changed Date: 2019-02-22 08:06:08 -0400 (Fri, 22 Feb 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gCrisprTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings gCrisprTools_1.11.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/gCrisprTools.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gCrisprTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gCrisprTools' version '1.11.2'
* 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 whether package 'gCrisprTools' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpU7sI9b/R.INSTALLc6041ed5625/gCrisprTools/man/ct.getPanther.Rd:16: file link 'PANTHER.db' in package 'PANTHER.db' does not exist and so has been treated as a topic
Warning: Package 'gCrisprTools' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/gCrisprTools.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 8.4Mb
sub-directories of 1Mb or more:
data 2.3Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'gCrisprTools-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ct.targetSetEnrichment
> ### Title: Test Whether a Specified Target Set is Enriched Within a Pooled
> ### Screen
> ### Aliases: ct.targetSetEnrichment
>
> ### ** Examples
>
> data(resultsDF)
> tar <- sample(unique(resultsDF$geneID), 20)
> res <- ct.targetSetEnrichment(resultsDF, tar)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
gCrisprTools
--- call from context ---
ct.targetSetEnrichment(resultsDF, tar)
--- call from argument ---
if (!(enrich %in% c(TRUE, FALSE))) {
stop("enrich must be either TRUE or FALSE.")
}
--- R stacktrace ---
where 1: ct.targetSetEnrichment(resultsDF, tar)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (summaryDF, targets, enrich = c(TRUE, FALSE), ignore = NULL)
{
if (!ct.resultCheck(summaryDF)) {
stop("Execution halted.")
}
if (!(enrich %in% c(TRUE, FALSE))) {
stop("enrich must be either TRUE or FALSE.")
}
valid <- intersect(targets, summaryDF$geneID)
if (length(valid) == 0) {
stop("None of the targets in the supplied vector are contained in the geneID column of the summary dataframe.")
}
if (length(setdiff(targets, valid)) != 0) {
warning(paste("Not all of the supplied targets are present in the geneID column of the summary dataframe. Proceeding with",
length(valid), "targets."))
}
summaryDF <- summaryDF[!duplicated(summaryDF$geneID), ]
summaryDF <- summaryDF[!is.na(summaryDF$geneID), ]
summaryDF <- summaryDF[!grepl("NoTarget", summaryDF$geneSymbol),
]
if (!is.null(ignore)) {
summaryDF <- summaryDF[!(summaryDF$geneID %in% ignore),
]
}
if (enrich) {
selected <- summaryDF[, c("Target-level Enrichment P",
"Target-level Enrichment Q")]
}
else {
selected <- summaryDF[, c("Target-level Depletion P",
"Target-level Depletion Q")]
}
row.names(selected) <- summaryDF$geneID
cuts <- c(0, 1/(10^(5:1)), 0.5, 1)
out <- list(targets = valid)
out$P.values <- cbind(cuts, vapply(cuts, function(x) {
sum(selected[valid, 1] <= x)
}, numeric(1)), vapply(cuts, function(x) {
.doHyperGInternal(length(valid), nrow(selected), sum(selected[,
1] <= x), sum(selected[valid, 1] <= x), TRUE)$p
}, numeric(1)))
out$Q.values <- cbind(cuts, vapply(cuts, function(x) {
sum(selected[valid, 2] <= x)
}, numeric(1)), vapply(cuts, function(x) {
.doHyperGInternal(length(valid), nrow(selected), sum(selected[,
2] <= x), sum(selected[valid, 2] <= x), TRUE)$p
}, numeric(1)))
colnames(out$P.values) <- colnames(out$Q.values) <- c("Cutoff",
"Sig", "Hypergeometric_P")
return(out)
}
<bytecode: 0x0812ffb0>
<environment: namespace:gCrisprTools>
--- function search by body ---
Function ct.targetSetEnrichment in namespace gCrisprTools has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
** running examples for arch 'x64' ... ERROR
Running examples in 'gCrisprTools-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ct.targetSetEnrichment
> ### Title: Test Whether a Specified Target Set is Enriched Within a Pooled
> ### Screen
> ### Aliases: ct.targetSetEnrichment
>
> ### ** Examples
>
> data(resultsDF)
> tar <- sample(unique(resultsDF$geneID), 20)
> res <- ct.targetSetEnrichment(resultsDF, tar)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
gCrisprTools
--- call from context ---
ct.targetSetEnrichment(resultsDF, tar)
--- call from argument ---
if (!(enrich %in% c(TRUE, FALSE))) {
stop("enrich must be either TRUE or FALSE.")
}
--- R stacktrace ---
where 1: ct.targetSetEnrichment(resultsDF, tar)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (summaryDF, targets, enrich = c(TRUE, FALSE), ignore = NULL)
{
if (!ct.resultCheck(summaryDF)) {
stop("Execution halted.")
}
if (!(enrich %in% c(TRUE, FALSE))) {
stop("enrich must be either TRUE or FALSE.")
}
valid <- intersect(targets, summaryDF$geneID)
if (length(valid) == 0) {
stop("None of the targets in the supplied vector are contained in the geneID column of the summary dataframe.")
}
if (length(setdiff(targets, valid)) != 0) {
warning(paste("Not all of the supplied targets are present in the geneID column of the summary dataframe. Proceeding with",
length(valid), "targets."))
}
summaryDF <- summaryDF[!duplicated(summaryDF$geneID), ]
summaryDF <- summaryDF[!is.na(summaryDF$geneID), ]
summaryDF <- summaryDF[!grepl("NoTarget", summaryDF$geneSymbol),
]
if (!is.null(ignore)) {
summaryDF <- summaryDF[!(summaryDF$geneID %in% ignore),
]
}
if (enrich) {
selected <- summaryDF[, c("Target-level Enrichment P",
"Target-level Enrichment Q")]
}
else {
selected <- summaryDF[, c("Target-level Depletion P",
"Target-level Depletion Q")]
}
row.names(selected) <- summaryDF$geneID
cuts <- c(0, 1/(10^(5:1)), 0.5, 1)
out <- list(targets = valid)
out$P.values <- cbind(cuts, vapply(cuts, function(x) {
sum(selected[valid, 1] <= x)
}, numeric(1)), vapply(cuts, function(x) {
.doHyperGInternal(length(valid), nrow(selected), sum(selected[,
1] <= x), sum(selected[valid, 1] <= x), TRUE)$p
}, numeric(1)))
out$Q.values <- cbind(cuts, vapply(cuts, function(x) {
sum(selected[valid, 2] <= x)
}, numeric(1)), vapply(cuts, function(x) {
.doHyperGInternal(length(valid), nrow(selected), sum(selected[,
2] <= x), sum(selected[valid, 2] <= x), TRUE)$p
}, numeric(1)))
colnames(out$P.values) <- colnames(out$Q.values) <- c("Cutoff",
"Sig", "Hypergeometric_P")
return(out)
}
<bytecode: 0x000000000e3b3a58>
<environment: namespace:gCrisprTools>
--- function search by body ---
Function ct.targetSetEnrichment in namespace gCrisprTools has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'unit.tests.R'
OK
** running tests for arch 'x64' ...
Running 'unit.tests.R'
OK
* 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: 2 ERRORs, 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/gCrisprTools.Rcheck/00check.log'
for details.