Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-26 15:05:14 -0500 (Fri, 26 Nov 2021).

CHECK results for CRISPRseek on tokay2

To the developers/maintainers of the CRISPRseek package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CRISPRseek.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 416/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.34.0  (landing page)
Lihua Julie Zhu
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/CRISPRseek
git_branch: RELEASE_3_14
git_last_commit: 11159db
git_last_commit_date: 2021-10-26 12:11:02 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CRISPRseek
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRISPRseek.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CRISPRseek_1.34.0.tar.gz
StartedAt: 2021-11-25 20:40:42 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 20:53:10 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 747.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: CRISPRseek.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRISPRseek.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CRISPRseek_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CRISPRseek/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CRISPRseek' version '1.34.0'
* 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 whether package 'CRISPRseek' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.9Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
* 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 ... NOTE
annotateOffTargets: no visible global function definition for 'exons'
annotateOffTargets: no visible global function definition for
  'seqlevels<-'
annotateOffTargets: no visible global function definition for 'genes'
predictRelativeFreqIndels : <anonymous>: no visible global function
  definition for 'predIndelFreq'
Undefined global functions or variables:
  exons genes predIndelFreq seqlevels<-
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:64-66: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:67-69: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:86-88: Dropping empty section \details
prepare_Rd: buildFeatureVectorForScoring.Rd:89-91: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:99-101: Dropping empty section \references
prepare_Rd: compare2Sequences.Rd:263-265: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:266-268: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:151-153: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:154-156: Dropping empty section \note
prepare_Rd: filtergRNAs.Rd:48-50: Dropping empty section \details
prepare_Rd: filtergRNAs.Rd:51-53: Dropping empty section \note
prepare_Rd: filtergRNAs.Rd:70-72: Dropping empty section \references
prepare_Rd: findgRNAs.Rd:306-308: Dropping empty section \references
prepare_Rd: getOfftargetScore.Rd:79-81: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:23-25: Dropping empty section \details
prepare_Rd: isPatternUnique.Rd:26-28: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:37-39: Dropping empty section \references
prepare_Rd: isPatternUnique.Rd:40-42: Dropping empty section \seealso
prepare_Rd: offTargetAnalysis.Rd:438-440: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:441-443: Dropping empty section \note
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:440-442: Dropping empty section \details
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:443-445: Dropping empty section \note
prepare_Rd: searchHits.Rd:99-101: Dropping empty section \details
prepare_Rd: searchHits.Rd:102-104: Dropping empty section \note
prepare_Rd: searchHits.Rd:130-132: Dropping empty section \references
prepare_Rd: searchHits2.Rd:116-118: Dropping empty section \details
prepare_Rd: searchHits2.Rd:119-121: Dropping empty section \note
prepare_Rd: searchHits2.Rd:152-154: Dropping empty section \references
prepare_Rd: translatePattern.Rd:22-24: Dropping empty section \details
prepare_Rd: translatePattern.Rd:25-27: Dropping empty section \note
prepare_Rd: translatePattern.Rd:33-35: Dropping empty section \references
prepare_Rd: translatePattern.Rd:36-38: Dropping empty section \seealso
prepare_Rd: uniqueREs.Rd:46-48: Dropping empty section \details
prepare_Rd: uniqueREs.Rd:49-51: Dropping empty section \note
prepare_Rd: uniqueREs.Rd:61-63: Dropping empty section \references
prepare_Rd: uniqueREs.Rd:64-66: Dropping empty section \seealso
prepare_Rd: writeHits.Rd:89-91: Dropping empty section \details
prepare_Rd: writeHits.Rd:92-94: Dropping empty section \note
prepare_Rd: writeHits2.Rd:99-101: Dropping empty section \details
prepare_Rd: writeHits2.Rd:102-104: Dropping empty section \note
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'CRISPRseek-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deepCpf1
> ### Title: DeepCpf1 Algorithm for predicting CRISPR-Cpf1 gRNA Efficacy
> ### Aliases: deepCpf1
> 
> ### ** Examples
> 
> library(keras)

Attaching package: 'keras'

The following object is masked from 'package:BiocGenerics':

    normalize

> library(mltools)
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:Biostrings':

    collapse, intersect, setdiff, setequal, union

The following object is masked from 'package:GenomeInfoDb':

    intersect

The following object is masked from 'package:XVector':

    slice

The following objects are masked from 'package:IRanges':

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

The following objects are masked from 'package:BiocGenerics':

    combine, intersect, setdiff, union

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(data.table)

Attaching package: 'data.table'

The following objects are masked from 'package:dplyr':

    between, first, last

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

> 
> use_implementation("tensorflow")
> 
> extendedSequence <- c('GTTATTTGAGCAATGCCACTTAATAAACATGTAA',
+  'TGACTTTGAATGGAGTCGTGAGCGCAAGAACGCT',
+  'GTTATTTGAGCAATGCCACTTAATAAACATGTAA',
+  'TGACTTTGAATGGAGTCGTGAGCGCAAGAACGCT')
> chrom_acc <- c(0,1, 0, 1)
> 
>  deepCpf1(extendedSequence = extendedSequence, chrom_acc = chrom_acc)
Error: Installation of Python not found, Python bindings not loaded.
Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment.
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'CRISPRseek-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deepCpf1
> ### Title: DeepCpf1 Algorithm for predicting CRISPR-Cpf1 gRNA Efficacy
> ### Aliases: deepCpf1
> 
> ### ** Examples
> 
> library(keras)

Attaching package: 'keras'

The following object is masked from 'package:BiocGenerics':

    normalize

> library(mltools)
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:Biostrings':

    collapse, intersect, setdiff, setequal, union

The following object is masked from 'package:GenomeInfoDb':

    intersect

The following object is masked from 'package:XVector':

    slice

The following objects are masked from 'package:IRanges':

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

The following objects are masked from 'package:BiocGenerics':

    combine, intersect, setdiff, union

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(data.table)

Attaching package: 'data.table'

The following objects are masked from 'package:dplyr':

    between, first, last

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

> 
> use_implementation("tensorflow")
> 
> extendedSequence <- c('GTTATTTGAGCAATGCCACTTAATAAACATGTAA',
+  'TGACTTTGAATGGAGTCGTGAGCGCAAGAACGCT',
+  'GTTATTTGAGCAATGCCACTTAATAAACATGTAA',
+  'TGACTTTGAATGGAGTCGTGAGCGCAAGAACGCT')
> chrom_acc <- c(0,1, 0, 1)
> 
>  deepCpf1(extendedSequence = extendedSequence, chrom_acc = chrom_acc)
Loaded Tensorflow version 2.0.0
2021-11-25 20:52:55.726645: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2
Error in py_call_impl(callable, dots$args, dots$keywords) : 
  ValueError: Error when checking input: expected input_2 to have 3 dimensions, but got array with shape (4, 1)

Detailed traceback:
  File "C:\Python37\lib\site-packages\tensorflow_core\python\keras\engine\training.py", line 909, in predict
    use_multiprocessing=use_multiprocessing)
  File "C:\Python37\lib\site-packages\tensorflow_core\python\keras\engine\training_arrays.py", line 715, in predict
    x, check_steps=True, steps_name='steps', steps=steps)
  File "C:\Python37\lib\site-packages\tensorflow_core\python\keras\engine\training.py", line 2472, in _standardize_user_data
    exception_prefix='input')
  File "C:\Python37\lib\site-packages\tensorflow_core\python\keras\engine\training_utils.py", line 565, in standardize_input_data
    'with shape ' + str(data_shape))
Calls: deepCpf1 ... predict.keras.engine.training.Model -> do.call -> <Anonymous> -> py_call_impl
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck/00check.log'
for details.


Installation output

CRISPRseek.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CRISPRseek_1.34.0.tar.gz && rm -rf CRISPRseek.buildbin-libdir && mkdir CRISPRseek.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CRISPRseek.buildbin-libdir CRISPRseek_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CRISPRseek_1.34.0.zip && rm CRISPRseek_1.34.0.tar.gz CRISPRseek_1.34.0.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
  4 10.5M    4  524k    0     0  1286k      0  0:00:08 --:--:--  0:00:08 1286k
 28 10.5M   28 3071k    0     0  2206k      0  0:00:04  0:00:01  0:00:03 2206k
 61 10.5M   61 6639k    0     0  2784k      0  0:00:03  0:00:02  0:00:01 2784k
100 10.5M  100 10.5M    0     0  3239k      0  0:00:03  0:00:03 --:--:-- 3240k

install for i386

* installing *source* package 'CRISPRseek' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CRISPRseek'
    finding HTML links ... done
    CRISPRseek-package                      html  
    annotateOffTargets                      html  
    buildFeatureVectorForScoring            html  
    calculategRNAEfficiency                 html  
    compare2Sequences                       html  
    deepCpf1                                html  
    filterOffTarget                         html  
    filtergRNAs                             html  
    findgRNAs                               html  
    getOfftargetScore                       html  
    isPatternUnique                         html  
    offTargetAnalysis                       html  
    offTargetAnalysisWithoutBSgenome        html  
    predictRelativeFreqIndels               html  
    searchHits                              html  
    searchHits2                             html  
    translatePattern                        html  
    uniqueREs                               html  
    writeHits                               html  
    writeHits2                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CRISPRseek' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CRISPRseek' as CRISPRseek_1.34.0.zip
* DONE (CRISPRseek)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CRISPRseek' successfully unpacked and MD5 sums checked

Tests output

CRISPRseek.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> #BiocGenerics:::testPackage("CRISPRseek")
> 
> proc.time()
   user  system elapsed 
   0.25    0.04    0.28 

CRISPRseek.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> #BiocGenerics:::testPackage("CRISPRseek")
> 
> proc.time()
   user  system elapsed 
   0.21    0.07    0.28 

Example timings

CRISPRseek.Rcheck/examples_i386/CRISPRseek-Ex.timings

nameusersystemelapsed
CRISPRseek-package210.61 7.24217.88
annotateOffTargets3.380.203.58
buildFeatureVectorForScoring0.080.000.07
calculategRNAEfficiency0.020.000.02
compare2Sequences7.100.127.23

CRISPRseek.Rcheck/examples_x64/CRISPRseek-Ex.timings

nameusersystemelapsed
CRISPRseek-package189.64 6.89196.53
annotateOffTargets3.320.163.47
buildFeatureVectorForScoring0.110.000.11
calculategRNAEfficiency0.020.000.01
compare2Sequences7.870.097.97