Back to Multiple platform build/check report for BioC 3.9
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for gCrisprTools on tokay2

This page was generated on 2019-04-09 12:27:13 -0400 (Tue, 09 Apr 2019).

Package 603/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 

Summary

Package: gCrisprTools
Version: 1.11.2
Command: 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
StartedAt: 2019-04-09 02:52:18 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:03:33 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 674.5 seconds
RetCode: 1
Status:  ERROR  
CheckDir: gCrisprTools.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   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
###
##############################################################################
##############################################################################


* 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.


Installation output

gCrisprTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/gCrisprTools_1.11.2.tar.gz && rm -rf gCrisprTools.buildbin-libdir && mkdir gCrisprTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gCrisprTools.buildbin-libdir gCrisprTools_1.11.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL gCrisprTools_1.11.2.zip && rm gCrisprTools_1.11.2.tar.gz gCrisprTools_1.11.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 7864k  100 7864k    0     0  58.0M      0 --:--:-- --:--:-- --:--:-- 61.4M

install for i386

* installing *source* package 'gCrisprTools' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gCrisprTools'
    finding HTML links ... done
    aln                                     html  
    ann                                     html  
    appendDateAndExt                        html  
    ct.DirectionalTests                     html  
    ct.GCbias                               html  
    ct.PRC                                  html  
    ct.PantherPathwayEnrichment             html  
    ct.ROC                                  html  
    ct.RRAaPvals                            html  
    ct.RRAalpha                             html  
    ct.RRAalphaBatch                        html  
    ct.alignmentChart                       html  
    ct.alphaBeta                            html  
    ct.applyAlpha                           html  
    ct.drawColorLegend                      html  
    ct.drawFlat                             html  
    ct.ecdf                                 html  
    ct.exprsColor                           html  
    ct.filterReads                          html  
    ct.gRNARankByReplicate                  html  
    ct.generateResults                      html  
    ct.getPanther                           html  
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
    ct.guideCDF                             html  
    ct.inputCheck                           html  
    ct.makeContrastReport                   html  
    ct.makeQCReport                         html  
    ct.makeReport                           html  
    ct.makeRhoNull                          html  
    ct.normalizeBySlope                     html  
    ct.normalizeGuides                      html  
    ct.normalizeMedians                     html  
    ct.normalizeNTC                         html  
    ct.normalizeSpline                      html  
    ct.numcores                             html  
    ct.prepareAnnotation                    html  
    ct.preprocessFit                        html  
    ct.rawCountDensities                    html  
    ct.resultCheck                          html  
    ct.stackGuides                          html  
    ct.targetSetEnrichment                  html  
    ct.topTargets                           html  
    ct.viewControls                         html  
    ct.viewGuides                           html  
    dir.writable                            html  
    es                                      html  
    essential.genes                         html  
    fit                                     html  
    gCrisprTools-package                    html  
    initOutDir                              html  
    renderReport                            html  
    resultsDF                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'gCrisprTools' is deprecated and will be removed from
  Bioconductor version 3.10
** testing if installed package can be loaded from final location
Warning: Package 'gCrisprTools' is deprecated and will be removed from
  Bioconductor version 3.10
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'gCrisprTools' ...
** testing if installed package can be loaded
Warning: Package 'gCrisprTools' is deprecated and will be removed from
  Bioconductor version 3.10
* MD5 sums
packaged installation of 'gCrisprTools' as gCrisprTools_1.11.2.zip
* DONE (gCrisprTools)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'gCrisprTools' successfully unpacked and MD5 sums checked

Tests output

gCrisprTools.Rcheck/tests_i386/unit.tests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

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.

> #require("BiocGenerics", quietly = TRUE)
> BiocGenerics:::testPackage("gCrisprTools")
PANTHER.db version 1.0.4


RUNIT TEST PROTOCOL -- Tue Apr 09 03:03:20 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gCrisprTools RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
Warning message:
Package 'gCrisprTools' is deprecated and will be removed from
  Bioconductor version 3.10 
> 
> proc.time()
   user  system elapsed 
   3.60    0.28    3.87 

gCrisprTools.Rcheck/tests_x64/unit.tests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

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.

> #require("BiocGenerics", quietly = TRUE)
> BiocGenerics:::testPackage("gCrisprTools")
PANTHER.db version 1.0.4


RUNIT TEST PROTOCOL -- Tue Apr 09 03:03:27 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gCrisprTools RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
Warning message:
Package 'gCrisprTools' is deprecated and will be removed from
  Bioconductor version 3.10 
> 
> proc.time()
   user  system elapsed 
   5.48    0.31    5.78 

Example timings

gCrisprTools.Rcheck/examples_i386/gCrisprTools-Ex.timings

nameusersystemelapsed
aln000
ann0.140.000.14
ct.DirectionalTests0.440.110.54
ct.GCbias7.560.287.85
ct.PRC1.300.061.36
ct.PantherPathwayEnrichment123.56 7.36165.21
ct.ROC0.170.080.25
ct.RRAaPvals0.520.210.73
ct.RRAalpha0.480.090.57
ct.alignmentChart0.000.020.02
ct.alphaBeta0.000.010.01
ct.ecdf000
ct.filterReads0.480.250.73
ct.gRNARankByReplicate0.820.181.00
ct.generateResults0.690.491.17
ct.guideCDF26.88 2.6429.53
ct.inputCheck0.150.010.17
ct.makeContrastReport 9.72 8.3318.80
ct.makeQCReport5.413.839.76
ct.makeReport17.4238.5656.66
ct.normalizeBySlope1.580.111.69
ct.normalizeGuides5.150.055.20
ct.normalizeMedians1.180.061.23
ct.normalizeNTC1.390.031.42
ct.normalizeSpline1.700.051.75
ct.prepareAnnotation0.990.051.03
ct.preprocessFit2.860.012.88
ct.rawCountDensities0.150.020.17
ct.resultCheck0.140.000.14
ct.stackGuides4.630.014.64

gCrisprTools.Rcheck/examples_x64/gCrisprTools-Ex.timings

nameusersystemelapsed
aln000
ann0.080.020.10
ct.DirectionalTests0.330.030.36
ct.GCbias6.630.196.81
ct.PRC1.110.031.14
ct.PantherPathwayEnrichment102.81 2.62105.44
ct.ROC0.160.000.16
ct.RRAaPvals0.340.000.34
ct.RRAalpha0.270.020.28
ct.alignmentChart000
ct.alphaBeta0.010.000.02
ct.ecdf000
ct.filterReads0.280.000.28
ct.gRNARankByReplicate0.610.000.61
ct.generateResults0.610.010.62
ct.guideCDF13.50 0.4113.91
ct.inputCheck0.080.000.08
ct.makeContrastReport 9.05 7.9517.62
ct.makeQCReport4.863.498.70
ct.makeReport14.2929.2044.04
ct.normalizeBySlope1.720.031.75
ct.normalizeGuides3.850.033.88
ct.normalizeMedians0.860.020.87
ct.normalizeNTC0.980.051.04
ct.normalizeSpline1.090.031.14
ct.prepareAnnotation0.570.010.57
ct.preprocessFit2.060.002.07
ct.rawCountDensities0.110.020.12
ct.resultCheck0.100.000.09
ct.stackGuides4.130.034.17