Question

error message with BiocManager::install on Mac console that's not on mac command line

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raf4 ▴ 30

@raf4-8249

Last seen 22 months ago

United States

Dear All,

I am using Bioconductor 3.9 with R 3.6.0 on Mac OS 10.14.4

When I try to install a program on the Mac Console I get

> BiocManager::install("org.Mm.eg.db")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'org.Mm.eg.db'
Error in res0[, "Package"] : subscript out of bounds

** testing if installed package keeps a record of temporary installation path
* DONE (org.Mm.eg.db)

When I run the same command on the command line it works.

> BiocManager::install("org.Mm.eg.db")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'org.Mm.eg.db'
also installing the dependencies ‘bit’, ‘prettyunits’, ‘bit64’, ‘blob’, ‘memois

.....

** testing if installed package keeps a record of temporary installation path
* DONE (org.Mm.eg.db)

I would appreciate any suggestions.

Thanks and best wishes, Richard Friedman

BiocManager Mac • 3.0k views

ADD COMMENT • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by raf4 ▴ 30

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What do you mean by the "Mac Console"?

ADD REPLY • link 5.4 years ago Steve Lianoglou ★ 13k

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Steve,

Sorry. I meanto to sat, "the RGUI".

Thanks and best wishes, Rich

ADD REPLY • link 5.4 years ago raf4 ▴ 30

Martin Morgan · Answer 1 · 2019-06-28

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

My best guess is that you have packages installed under R version 3.5 and packages installed under R version 3.6 in the same library. What does

BiocManager::valid()

have to say? Does corrrecting any issues suggested there resolve the problem?

ADD COMMENT • link 5.4 years ago Martin Morgan 25k

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Martin,

In the RGUI I got

> BiocManager::valid()
Error in res0[, "Package"] : subscript out of bounds
On the command line I got:

Bioconductor version '3.9'

  * 2 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "rgl", "rtracklayer"
  ), update = TRUE, ask = FALSE)

These are 2 programs that required compilation and I ran into trouble, so I used an older version: Here is an excerpt (because of length(from when I tried to compile them:

> BiocManager::install(c(
+     "rgl", "rtracklayer"
+   ), update = TRUE, ask = FALSE)
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'rgl', 'rtracklayer'

  There are binary versions available but the source versions are later:
              binary   source needs_compilation
rgl         0.100.19 0.100.24              TRUE
rtracklayer   1.43.3   1.44.0              TRUE

Do you want to install from sources the packages which need compilation? (Yes/no/cancel) Yes
installing the source packages ‘rgl’, ‘rtracklayer’

...

* installing *source* package ‘rgl’ ...
** package ‘rgl’ successfully unpacked and MD5 sums checked
** using staged installation
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Does this give you any clues?

Thanks and best wishes, Rich

ADD REPLY • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by raf4 ▴ 30

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I haven't used the R Gui in a long while, is it possible that it's loading something into your workspace on startup that launching R from terminal isn't?

To test that you can quit the R gui, then start it again and see what the output of running ls() in a fresh R session gives? should be nothing ...

ADD REPLY • link 5.4 years ago Steve Lianoglou ★ 13k

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...for instance, is .libPaths() different in the two environments?

ADD REPLY • link 5.4 years ago Martin Morgan 25k

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Steve and Martin,

Thank you for your help.

> ls()
character(0)

in both the Gui and the command line

> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"

ib both the GUI and the command line.

I looked into the missing xcrun program noted above.

I got the following:

Richards-Mini:~ epiktistes$ cd /Library/Developer/CommandLineTools/usr/bin/xcrun
-bash: cd: /Library/Developer/CommandLineTools/usr/bin/xcrun: No such file or directory

I have

/Library/Developer/CommandLineTools/usr

but no bin in that directory

here is all I have there:

Richards-Mini:usr epiktistes$ ls
share
Richards-Mini:usr epiktistes$ ls share
man

I think that this may be solved by installing xcode. I will try that later this week and let you know how it went.

Best wishes, Rich

ADD REPLY • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by raf4 ▴ 30

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Dear Martin and Steve and List,

I installed xcode and I know can install everything in the command line but not in the RGUI. Here is the command line:

> BiocManager::install("rgl")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'rgl'
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rgl_0.100.24.tgz'
Content type 'application/x-gzip' length 4765007 bytes (4.5 MB)
==================================================
downloaded 4.5 MB


The downloaded binary packages are in
    /var/folders/7_/51c4cqhx4g5bsdnwkzrnv1fr0000gn/T//RtmpHdbnO6/downloaded_packages
>

Here is the RGUI

> BiocManager::install("rgl")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'rgl'
Error in readRDS(dest) : unknown input format
>

I would appreciate any suggestions.

Thanks and best wishes, Rich

ADD REPLY • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by raf4 ▴ 30

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Also, I had tried the following

Command line

> BiocManager::valid()
[1] TRUE
R

Gui

> BiocManager::valid()
Error in readRDS(dest) : unknown input format

ADD REPLY • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by raf4 ▴ 30

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You could try to debug this on your end, by saying

trace(readRDS, quote(print(file)))
BiocManager::valid()

This will print out a number of files, the last file printed will be the one that is causing problems. It will either be a temporary file with a directory Rtmp.... somewhere in the file path, or a package file with <package name>/Mega/package.rds. For the later you should use remove.packages() to remove the package, and repeat BiocManager::valid(). For the former you should restart your R session, being sure to start R with the --vanilla option / without referencing previous RData, etc files.

ADD REPLY • link 5.4 years ago Martin Morgan 25k

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Martin,

Thanks. Here is the last line I got in the RGUI and my attempt to remove the package:

> remove.packages("repos_http%3A%2F%2Fwatson.nci.nih.gov%2Fcran_mirror%2Fsrc%2Fcontrib.rds")
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
(as ‘lib’ is unspecified)
Error in find.package(pkgs, lib) : 
  there is no package called ‘repos_http%3A%2F%2Fwatson.nci.nih.gov%2Fcran_mirror%2Fsrc%2Fcontrib.rds’
> remove.packages("/var/folders/7_/51c4cqhx4g5bsdnwkzrnv1fr0000gn/T//RtmprZqqJT/repos_http%3A%2F%2Fwatson.nci.nih.gov%2Fcran_mirror%2Fsrc%2Fcontrib.rds")
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
(as ‘lib’ is unspecified)
Error in find.package(pkgs, lib) : 
  there is no package called ‘/var/folders/7_/51c4cqhx4g5bsdnwkzrnv1fr0000gn/T//RtmprZqqJT/repos_http%3A%2F%2Fwatson.nci.nih.gov%2Fcran_mirror%2Fsrc%2Fcontrib.rds’
>

I received no error message in the R command line.

I closed the RGui and quit the R command lines. I restarted the R command line with --vanilla. Here is the command on the command line:

> BiocManager::valid()
[1] TRUE
>

I restarted the GUI and tried the command;

 > BiocManager::valid()
Error in res0[, "Package"] : subscript out of bounds

Please advise.

Thanks and best wishes, Rich

ADD REPLY • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by raf4 ▴ 30

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Please follow instructions closely. The path that you are using remove.package() on is not the path to an installed package, but rather a temporary file. Simply restarting R would result in a different temporary file.

Also, please take a few minutes to review how to format your posts, especially highlighting code chunks and pressing the button with 101/010 in the support site editor. Look at the preview to verify that the content is legible (the legibility of your current posts is because I or others have edited them after the fact).

The information that you post does point to one feature that you might reconsider. Apparently you have selected 'watson.nci.nih.gov' as your CRAN repository. I suggest using the canonical location cran.r-project.org.

Let's stop referencing the command line, which seems to be working.

In the R gui, after the error occurs, use the command traceback() to provide more context about where the error occurs.

BiocManager::valid() # error occurs, so then...
traceback()

ADD REPLY • link 5.4 years ago Martin Morgan 25k

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Martin, I followed your instructions above. I had to compile one remaining program from source and then BiocManager::install worked from the GUI. Thank you for your help and patience. I will observe formatting guidelines more carefully in the future.

Best wishes, Rich

ADD REPLY • link 5.4 years ago raf4 ▴ 30