Install error

[cristinarodrig]

I am trying to install and keep getting this error. Any solutions on how to fix this?

[ajitjohnson]

It looks like the latest version of the XML package requires R V.4 or above.

Try this to install the previous version of XML like below

packageUrl<- "https://cran.r-project.org/src/contrib/Archive/XML/XML_3.99-0.3.tar.gz"
install.packages(packageUrl, repos=NULL, type='source')

Let me know if it works.

[cristinarodrig]

That did work! Thank you. I am now getting this error when I run my data. I am getting a folder downloaded but it's not giving me the differential expression that I am looking for.

[ajitjohnson]

I've never got that error before. Can you paste screenshot of your data and your metadata?

[cristinarodrig]

I had someone run the same files as well and they were able to get the differential expressions file so I'm not sure what's missing on my end.

[ajitjohnson]

Ah, I see what the problem is. The Gene names need to be either Entrez id or HUGO gene name.

Did someone else who ran this dataset previously, run it a while back? The step you are receiving the error now is a new function that I added recently (probably a week before).

[pavitraviswanath]

Hi Ajit. I am also having trouble installing Arseq. This is the error I am getting:

[ajitjohnson]

Can you update your ComplexHeatmap package and try again. It looks like that may be an error.

[poconnel3]

I am also having an install error on a 64bit Mac. Manually updated ComplexHeatmaps first, but now it is trying to install DO.db package that neither it, nor I can find. Also, this package used to run on my computer about a year ago.

installing *source* package ‘rprojroot’ ...
** package ‘rprojroot’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* DONE (rprojroot)
* installing *source* package ‘DO.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package ‘AnnotationDbi’ was built under R version 4.0.2
Execution halted
ERROR: lazy loading failed for package ‘DO.db’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/DO.db’
Error: Failed to install 'arseq' from GitHub:
  (converted from warning) installation of package ‘DO.db’ had non-zero exit status

[maitra]

I don't know if this package is still supported but I get an error in installation:

> devtools::install_github( "ajitjohnson/arseq", INSTALL_opts = "--no-multiarch")
Downloading GitHub repo ajitjohnson/arseq@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
   checking for file ‘/tmp/RtmpTIKMC3/remotes42cc8df97716/ajitjohnson-arseq-5da1✔  checking for file ‘/tmp/RtmpTIKMC3/remotes42cc8df97716/ajitjohnson-arseq-5da1377/DESCRIPTION’
─  preparing ‘arseq’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘arseq_2.3.2.tar.gz’
   
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘arseq’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class “ident”; class definition removed from ‘dbplyr’
Execution halted
ERROR: lazy loading failed for package ‘arseq’
* removing ‘/usr/lib64/R/library/arseq’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpTIKMC3/file42cc83a32194a/arseq_2.3.2.tar.gz’ had non-zero exit status
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