joda 1.36.0
Ewa Szczurek
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/joda |
| Branch: RELEASE_3_11 |
| Last Commit: c7cd68c |
| Last Changed Date: 2020-04-27 14:24:22 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:joda.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings joda_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/joda.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'joda/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'joda' version '1.36.0'
* 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 whether package 'joda' 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 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 ... NOTE
Packages in Depends field not imported from:
'RBGL' 'bgmm'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
infer.probabilities: no visible global function definition for 'par'
infer.probabilities : getProbs: no visible global function definition
for 'unsupervised'
infer.probabilities : getProbs: no visible global function definition
for 'DEprobs'
infer.probabilities : getProbs: no visible global function definition
for 'belief'
infer.probabilities : getProbs: no visible global function definition
for 'title'
infer.probabilities : getProbs: no visible global function definition
for 'legend'
regulation.scores: no visible global function definition for 'as'
regulation.scores: no visible global function definition for
'transitive.closure'
Undefined global functions or variables:
DEprobs as belief legend par title transitive.closure unsupervised
Consider adding
importFrom("graphics", "legend", "par", "title")
importFrom("methods", "as")
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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'joda-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: differential.probs
> ### Title: Calculating probabilities of differential expression in
> ### perturbation experiments
> ### Aliases: differential.probs
>
> ### ** Examples
>
>
> data(damage)
>
> # Get the probabilities of differential expression
> # for the knockout of p53 in healthy cells
> probs.healthy.p53= differential.probs(data.healthy[,"p53",FALSE],
+ beliefs.healthy["p53"], TRUE,TRUE)
joda: Input correctly defined
Inferring probabilities of differential expression under the knockdown of p53 ...
Applying belief-based mixture modeling
The parameters of the model for p53:
differential unchanged
Mixing proportions: 0.50634787 0.493652126
Means: 0.05503342 -0.072353721
Variances: 0.04807592 0.007986199
>
> # Get the probabilities of differential expression
> # for the knockout of Ste12 under pheromone treatment
> library(bgmm)
> data(Ste12)
> data=as.matrix(Ste12Data)
> colnames(data)="Ste12"
> beliefs=list(Ste12=Ste12Beliefs)
> diff.p=differential.probs(data,beliefs,TRUE,TRUE)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
joda
--- call from context ---
sanity.check.beliefs(data, beliefs)
--- call from argument ---
if (!class(data) %in% c("matrix", "data.frame")) stop(paste("\ndifferential.probs Error: data must be a matrix."))
--- R stacktrace ---
where 1: sanity.check.beliefs(data, beliefs)
where 2: differential.probs(data, beliefs, TRUE, TRUE)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, beliefs)
{
if (is.null(beliefs))
beliefs = list()
if (!class(data) %in% c("matrix", "data.frame"))
stop(paste("\ndifferential.probs Error: data must be a matrix."))
if (!class(beliefs) == "list")
stop(paste("\ndifferential.probs Error: beliefs must be a list."))
regs = colnames(data)
c1 <- all(names(beliefs) %in% regs)
if (!c1)
stop(paste("\ndifferential.probs Error: beliefs must be a list of matrices, with names as subset of the data columns (regulators)."))
ck <- function(kn) {
k = beliefs[[kn]]
OK <- TRUE
if (!is.null(k)) {
if (!is.matrix(k)) {
cat(" \n Error:. For a given regulator, the beliefs must be given as a matrix\n")
return(FALSE)
}
gens = rownames(data)
if (!all(rownames(k) %in% gens)) {
cat("\n Error: the rownames of the belief matrices must be a subset of the rownames of the data'\n")
return(FALSE)
}
if (!ncol(k) %in% c(2, 3)) {
cat("\n Error: the belief matrices must have either two or three columns\n")
return(FALSE)
}
OK <- all(k <= 1)
OK <- all(k >= 0)
OK <- all(apply(k, 1, sum) == 1)
if (!OK)
cat("\n Error: the belief matrices must have values in (0,1), each row being a distribution over the columns.\n")
}
OK
}
c2 <- all(sapply(regs, ck))
if (!(c2))
stop("")
}
<bytecode: 0x0b69be28>
<environment: namespace:joda>
--- function search by body ---
Function sanity.check.beliefs in namespace joda has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
** running examples for arch 'x64' ... ERROR
Running examples in 'joda-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: differential.probs
> ### Title: Calculating probabilities of differential expression in
> ### perturbation experiments
> ### Aliases: differential.probs
>
> ### ** Examples
>
>
> data(damage)
>
> # Get the probabilities of differential expression
> # for the knockout of p53 in healthy cells
> probs.healthy.p53= differential.probs(data.healthy[,"p53",FALSE],
+ beliefs.healthy["p53"], TRUE,TRUE)
joda: Input correctly defined
Inferring probabilities of differential expression under the knockdown of p53 ...
Applying belief-based mixture modeling
The parameters of the model for p53:
differential unchanged
Mixing proportions: 0.50634787 0.493652126
Means: 0.05503342 -0.072353721
Variances: 0.04807592 0.007986199
>
> # Get the probabilities of differential expression
> # for the knockout of Ste12 under pheromone treatment
> library(bgmm)
> data(Ste12)
> data=as.matrix(Ste12Data)
> colnames(data)="Ste12"
> beliefs=list(Ste12=Ste12Beliefs)
> diff.p=differential.probs(data,beliefs,TRUE,TRUE)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
joda
--- call from context ---
sanity.check.beliefs(data, beliefs)
--- call from argument ---
if (!class(data) %in% c("matrix", "data.frame")) stop(paste("\ndifferential.probs Error: data must be a matrix."))
--- R stacktrace ---
where 1: sanity.check.beliefs(data, beliefs)
where 2: differential.probs(data, beliefs, TRUE, TRUE)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (data, beliefs)
{
if (is.null(beliefs))
beliefs = list()
if (!class(data) %in% c("matrix", "data.frame"))
stop(paste("\ndifferential.probs Error: data must be a matrix."))
if (!class(beliefs) == "list")
stop(paste("\ndifferential.probs Error: beliefs must be a list."))
regs = colnames(data)
c1 <- all(names(beliefs) %in% regs)
if (!c1)
stop(paste("\ndifferential.probs Error: beliefs must be a list of matrices, with names as subset of the data columns (regulators)."))
ck <- function(kn) {
k = beliefs[[kn]]
OK <- TRUE
if (!is.null(k)) {
if (!is.matrix(k)) {
cat(" \n Error:. For a given regulator, the beliefs must be given as a matrix\n")
return(FALSE)
}
gens = rownames(data)
if (!all(rownames(k) %in% gens)) {
cat("\n Error: the rownames of the belief matrices must be a subset of the rownames of the data'\n")
return(FALSE)
}
if (!ncol(k) %in% c(2, 3)) {
cat("\n Error: the belief matrices must have either two or three columns\n")
return(FALSE)
}
OK <- all(k <= 1)
OK <- all(k >= 0)
OK <- all(apply(k, 1, sum) == 1)
if (!OK)
cat("\n Error: the belief matrices must have values in (0,1), each row being a distribution over the columns.\n")
}
OK
}
c2 <- all(sapply(regs, ck))
if (!(c2))
stop("")
}
<bytecode: 0x000000000feb0248>
<environment: namespace:joda>
--- function search by body ---
Function sanity.check.beliefs in namespace joda has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
* 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/joda.Rcheck/00check.log'
for details.