Software installation error

Question

[amy16]

Hi, I am unable to install the GenomeInfoDbData package from Bioconductor project in Rstudio. Following is the error message: 'C:\Program' is not recognized as an internal or external command, operable program or batch file.

Any help is appreciated. Thanks in advance.

[Sean Davis]

How are you trying to install the package? And what OS are you using?

[amy16]

I have Rstudio installed on Windows operating system. I used the following command line for installation.

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

Answer 1

[h.mon]

The (more complete) error message you reported on a previous thread indicates you are trying to install the package on a network file share. Two suggestions were given at the BioConductor Biostars thread (which you read):

1) do not use a network shared folder to install.

2) map the network shared folder to a letter.

Did you try them? Also, asking the same question and providing less details than before is kind of wasteful of everybody's time (yours and ours).

[amy16]

Yes I had tried to use the local machine drive. It still doesn't work. I keep getting the same error. installation of package ‘C:/Program Files/RStudio/R/R/WIN-LI~1/3.4/GenomeInfoDbData_0.99.1.tar.gz’ had non-zero exit status

[h.mon]

Output of sessionInfo()?

[amy16]

sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 [4] LC_NUMERIC=C LC_TIME=English_Australia.1252

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

loaded via a namespace (and not attached): [1] compiler_3.4.2 IRanges_2.12.0 parallel_3.4.2 tools_3.4.2 RCurl_1.95-4.8
[6] S4Vectors_0.16.0 BiocGenerics_0.24.0 bitops_1.0-6 stats4_3.4.2

[h.mon]

Another suggestion from this thread: you must install the Rtools package.

Also, you may have problems with spaces on your PATH ("C:/Program Files/R/R-34~1.2/bin/x64/R"), although I would think spaces shouldn't cause problems, as R is installed in Program Files since times immemorial.

So, try to:

1) install Rtools (install.packages("Rtools")

2) install GenomeInfoDbData

If that fails, try setting a library folder on your local drive and without spaces, then try to install GenomeInfoDbData again.

[amy16]

install.packages("Rtools") Installing package into ‘C:/Users/a123456/RStudio-1.1.383/R/downloaded_packages’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘Rtools’ is not available (for R version 3.4.2)

To install packages in C drive program files, the system asks for the administrator rights and so it defaults downloads it into users account. I tried changing the environment variable in order to change the library path. It doesn't seem to work. I copying the downloaded packages into the C:Program Files and still doesn't work.

I will be very much grateful if someone could provide me with detailed instruction of installing Ballgown irrespective of if it can be in a desktop or on a HPC. Thanks in Advance.

[h.mon]

I will be very much grateful if someone could provide me with detailed instruction of installing Ballgown irrespective of if it can be in a desktop or on a HPC.

I just installed R and ballgown on a windows laptop. After installing R, just:

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

Rtools was not needed. I also installed ballgown on a linux server, logged as regular user:

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

Your problem is trying to install on a network file share. The computers you have access have privileged (admin) and unprivileged (regular users) accounts, regular users home is on a network file share: all this points to the existence of a system administrator.

To install packages in C drive program files, the system asks for the administrator rights

So (nicely) ask your system administrator to install ballgown system-wide. Doing so is probably part of his job, and sysadmins don't bite.

[amy16]

Ok, I did this with ballgown package. Then when I try to load the ballgown package, it said it requires Biocgenerics package and when I tried installing it from local drive C:ProgramFiles into Rstudio because the default lib path in Rstudio is set to users drive (C: Users/a123456/). When I try to change this path, the Rstudio does not accept the change.