Search
Question: ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
0
gravatar for phpaul2010
16 months ago by
phpaul20100
phpaul20100 wrote:

Trying to install bioClite 3.2 onto R 3.2.2 using

biocLite("tgirke/systemPipeR", build_vignettes=TRUE, dependencies=TRUE)

this appears to install all the packages then fails as

* checking for file 'C:...\Temp\Rtmpmm0BY2\devtools278c2297552f\tgirke-systemPipeR-4b48c46/DESCRIPTION' ... OK
* preparing 'systemPipeR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
Warning: running command '"C:/PROGRA~1/R/R-32~1.2/bin/x64/Rcmd.exe" INSTALL -l "C:....\Temp\RtmpYF4EL9\Rinst1e543dcb4481" --no-multiarch "C:/..../Temp/RtmpYF4EL9/Rbuild1e544bb64e5d/systemPipeR"' had status 1
      -----------------------------------
ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
* removing 'C:/..../Temp/RtmpYF4EL9/Rinst1e543dcb4481/systemPipeR'

biocValid() finds only the the R-package curl is possibly out of date the curl version is 0.9.7 given as built under R version 3.2.5, I am running R 3.2.2

> traceback()
14: stop("Command failed (", status, ")", call. = FALSE)
13: fun(r, args = args, env_vars = env_vars, path = path, ...)
12: R(cmd, path, quiet = quiet)
11: force(code)
10: withr::with_temp_libpaths(R(cmd, path, quiet = quiet))
9: build(pkg, tempdir(), vignettes = build_vignettes, quiet = quiet)
8: install(source, ..., quiet = quiet, metadata = metadata)
7: FUN(X[[i]], ...)
6: vapply(remotes, install_remote, ..., FUN.VALUE = logical(1))
5: install_remotes(remotes, quiet = quiet, ...)
4: devtools::install_github(doing, ...)
3: .githubInstall(todo, ...)
2: .biocLiteInstall(pkgs, ask = ask, siteRepos = siteRepos, suppressUpdates = suppressUpdates, 
       ...)
1: biocLite("tgirke/systemPipeR", build_vignettes = TRUE, dependencies = TRUE)

Any suggestions would be appreciated.

ADD COMMENTlink modified 16 months ago • written 16 months ago by phpaul20100
1

Presumably this is actually a problem with GO.db or one if its dependencies.  Do you get an error message when you install it directly? 

source("https://bioconductor.org/biocLite.R")
biocLite("GO.db")
ADD REPLYlink written 16 months ago by Mike Smith2.1k
0
gravatar for phpaul2010
16 months ago by
phpaul20100
phpaul20100 wrote:

Thanks for the suggestion, since my entry, I installed R 3.3.1 and updated all the R libraries, now I get

> biocLite("tgirke/systemPipeR", build_vignettes=TRUE, dependencies=TRUE)    
.
.
.
ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
* removing 'C:/.../Local/Temp/RtmpGGgCOK/Rinst2b98b35608/systemPipeR'

I followed with

> biocValid()

* sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] httr_1.2.1           curl_1.0             BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] R6_2.1.2        tools_3.3.1     withr_1.0.2     memoise_1.0.0   knitr_1.13      git2r_0.15.0   
[7] digest_0.6.9    devtools_1.12.0

* Out-of-date packages
                Package           LibPath                                       Installed Built   ReposVer 
GenomicFeatures "GenomicFeatures" "C:/.../R/win-library/3.3" "1.24.4"  "3.3.1" "1.24.5" 
limma           "limma"           "C:/.../R/win-library/3.3" "3.28.14" "3.3.1" "3.28.16"
                Repository                                              
GenomicFeatures "https://bioconductor.org/packages/3.3/bioc/src/contrib"
limma           "https://bioconductor.org/packages/3.3/bioc/src/contrib"

update with biocLite()

Error: 2 package(s) out of date
> biocLite()

.

.

* installing *source* package 'BiocParallel' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (BiocParallel)
* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (GenomicFeatures)

The downloaded source packages are in
	‘C:\...\Local\Temp\RtmpYRC5io\downloaded_packages’
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.3.1/library"' is not writable
Error in install.packages(update[instlib == l, "Package"], l, repos = repos,  : 
  unable to install packages

on your suggestion

> biocLite("GO.db")

.

.

The downloaded binary packages are in
	C:\...\Local\Temp\RtmpYRC5io\downloaded_packages
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.3.1/library"' is not writable
Error in install.packages(update[instlib == l, "Package"], l, repos = repos,  : 
  unable to install packages

 

Seems like I cannot write to the directory required....

 

ADD COMMENTlink written 16 months ago by phpaul20100
0
gravatar for Thomas Girke
16 months ago by
Thomas Girke1.6k
United States
Thomas Girke1.6k wrote:

A few suggestions. First, you want to resolve your permission issue on your system for installing packages (e.g. run with admin permissions). After this please install systemPipeR like any other Bioconductor package with:

source("https://bioconductor.org/biocLite.R")
biocLite("systemPipeR")

A few suggestions related to NGS analysis on Windows. While many analysis steps will run fine in systemPipeR on Windows, alignments and other steps depending on external software are unlikely to work. The only R/Bioconductor software I know that supports NGS alignments on Windows is QuasR.

Thomas 

ADD COMMENTlink written 16 months ago by Thomas Girke1.6k
0
gravatar for phpaul2010
16 months ago by
phpaul20100
phpaul20100 wrote:

Thank you for the input. I added a pointer to a personnel library in the .Rlogin. I proceeded as

> source("https://bioconductor.org/biocLite.R")
> biocLite("systemPipeR")

I allowed to update all and to save in personnel library, this seemed to execute

> biocValid()

I was informed some libraries were out of date

> biocLite()

I allowed to update all to save in personnel library, this seemed to execute

> library(systemPipeR)
Loading required package: ShortRead
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘hwriter’
Error: package ‘ShortRead’ could not be loaded

Any suggestions would be useful. I will try to get admin privileges and try again. I suspect the mixing of personnel and system libraries was a bad idea and is probably messing up the install.

Otherwise, probably have spent enough effort trying to get this to work. I need to move on and try other options. Any information on how to clean off the machine would be useful. Thanks for any help.

 

ADD COMMENTlink written 16 months ago by phpaul20100
0
gravatar for phpaul2010
16 months ago by
phpaul20100
phpaul20100 wrote:

I have installed CRAN's hwriter and now get

> library(systemPipeR)
Loading required package: ShortRead
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘Category’
Error: package or namespace load failed for ‘systemPipeR’
> biocLite("Category")
> library(systemPipeR)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘xtable’
Error: package or namespace load failed for ‘systemPipeR’

I have installed CRAN's xtable and now get

> library(systemPipeR)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘AnnotationForge’
Error: package or namespace load failed for ‘systemPipeR’

Does this go on for much longer? Is there a list that I could use to do this in bulk? Will I need to do this all again if I restart R?

ADD COMMENTlink written 16 months ago by phpaul20100
0
gravatar for Thomas Girke
16 months ago by
Thomas Girke1.6k
United States
Thomas Girke1.6k wrote:

You need to fix your R installation or nothing will work. Getting admin permissions for the system you are on may simplify this task.   

ADD COMMENTlink written 16 months ago by Thomas Girke1.6k
0
gravatar for phpaul2010
16 months ago by
phpaul20100
phpaul20100 wrote:

Just to continue

> biocLite("AnnotationForge")

> library(systemPipeR)

  there is no package called ‘BBmisc’

> install.packages("BBmisc")

> library(systemPipeR)

  there is no package called ‘fail’

> install.packages("fail")

> library(systemPipeR)

  there is no package called ‘sendmailR’

> install.packages("sendmailR")

> library(systemPipeR)

> library(systemPipeRdata)

  there is no package called ‘systemPipeRdata’

> biocLite("systemPipeRdata")

.

.

The downloaded source packages are in

        ‘C:\Users\paul28\AppData\Local\Temp\Rtmpmw4G7W\downloaded_packages’

Old packages: 'XVector', 'mgcv', 'survival'

Update all/some/none? [a/s/n]:

a

 

  There is a binary version available but the source version is later:

        binary source needs_compilation

XVector 0.12.0 0.12.1              TRUE

 

  Binaries will be installed

Warning: package ‘XVector’ is in use and will not be installed

Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :

  'lib = "C:/Program Files/R/R-3.3.1/library"' is not writable

 

The result is that R locks up and will not be restarted from RStudio

 

ADD COMMENTlink written 16 months ago by phpaul20100

It might help to go backward

remove.pacakges("systemPipeR")

(repeat until R says there is no package to remove). Make sure that the first entry in .libPaths() can be written by your user. Then go forward

biocLite("systemPipeR")

again making sure that the first entry in .libPaths() is writable. Do each step in a brand-new R session, with no non-base packages loaded -- something like

> search()
[1] ".GlobalEnv"        "package:stats"     "package:graphics" 
[4] "package:grDevices" "package:utils"     "package:datasets" 
[7] "package:methods"   "Autoloads"         "package:base"    
ADD REPLYlink modified 16 months ago • written 16 months ago by Martin Morgan ♦♦ 20k
0
gravatar for Thomas Girke
16 months ago by
Thomas Girke1.6k
United States
Thomas Girke1.6k wrote:

Sorry about the frustration, but this will all go away if you can fix your R/Bioc install. In a functional environment, biocLite() will install all dependency package for you automatically and you only need to do this once. On Windows (and OS X) these installs are also very fast since pre-compiled binaries are used. If you have insufficient permissions on your current system then perhaps contact the admin of that computer or try it on another computer. 

ADD COMMENTlink written 16 months ago by Thomas Girke1.6k
0
gravatar for phpaul2010
16 months ago by
phpaul20100
phpaul20100 wrote:

I used .Rlogin to add a writeable first entry in .libPaths. After a few more try/add code element/tray again I can actually run the package.

I have been following the text/instructions in VAR-Seq workflow template: Some Descriptive Title of May 15,2016

The first issue was with the command

args<-systemArgs(sysma = "param/trimPE/param", mytargets="targetsPE.txt")[1:4]

The file targetPE.txt point at ./data/... but the files are actually in ./data/fastq/...

The second issue was with the command

args <- systemArgs(sysma="bwa.param", mytargets="targets.txt")

The file bwa.param is not found, so I am tryign to sort that one

Is there a better set of text/instructions that I should be referring to

ADD COMMENTlink written 16 months ago by phpaul20100

I recommend working through the main manual (HTML Overview Vignette here) first which explains the overall concepts of the workflows and the expected directory structure. 

The additional subdirectory you mention above is generated by genWorkenvir() on Windows only. I definitely will fix this inconsistency asap. As a temporary workaround on Windows you may want to run the following commands from your R session. This should move the input files to the expected location:

file.copy(list.files("data/fastq/", "*", full.names=TRUE), "data")
file.copy(list.files("data/annotation/", "*", full.names=TRUE), "data", recursive=TRUE)
file.copy(list.files("results/bam/", "*", full.names=TRUE), "results")

As for running the VAR-Seq workflow on Windows please be aware that there are several steps where either the corresponding R packages (gmapR/VariantTools) or external software (BWA/GATK) are not supported on Windows. This means that you would need to run the alignments and variant calling steps on a Linux or OS X system. Most of the upstream and downstream steps should work on Windows.

ADD REPLYlink modified 16 months ago • written 16 months ago by Thomas Girke1.6k
0
gravatar for phpaul2010
16 months ago by
phpaul20100
phpaul20100 wrote:

Thank you.

I fixed the file path issue by editing the target files to the full path.

I did find and switched to working from the Overview Vignette. Very useful.

I did manage to crash Rstudio by resizing the plot window when executing seeFastqPlot(fqlist)but I think that may be a normal response during a large plot.

The note about packages not supported under R-windows is useful.

Thank you for all of your assistance.

ADD COMMENTlink written 16 months ago by phpaul20100

RStudio crashes as a result of resizing the plotting window are not uncommon. As shown in the vignette(s), redirecting the seeFastq output to image files with pdf() or png() rather than viewing them in RStudio is highly recommended since those plots can get really large, especially if you want to compare the results of many fastq files next to each other. A PDF viewer or web browser (for png) are often the better tools for zooming into large images.  

As for NGS analysis on Windows, perhaps the new windows subsystem for linux (WSL) will simplify things in the future? 

ADD REPLYlink written 16 months ago by Thomas Girke1.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 179 users visited in the last hour