Comments (9)
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.
from arseq.
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.
from arseq.
I've never got that error before. Can you paste screenshot of your data and your metadata?
from arseq.
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.
from arseq.
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).
from arseq.
Hi Ajit. I am also having trouble installing Arseq. This is the error I am getting:
from arseq.
Can you update your ComplexHeatmap
package and try again. It looks like that may be an error.
from arseq.
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
from arseq.
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
>
from arseq.
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from arseq.