This library does not load

[maxbox63]

Thank you for providing this set of repositories and the normalization testing package. I am interested in comparing the Network Centrality Scaling approach to TMM, and have been able to load the lymphoma data for this purpose. However, I have not been able to load this package, even though the two packages have similar instructions. This package appears to contain .rda files, not .rds files, for the relevant data. I am not very familiar with Bioconductor or with .rda files, and I am not able to overcome this error. Could you please update this data so that it loads properly?

To be specific, neither of the first two lines of the following code chunk from the README.md succeeds without error:

devtools::install_github('ttdtrang/data-rnaseq-sarcoma')
data(sarcoma.rnaseq.gene, package='data.rnaseq.sarcoma')
dim(sarcoma.rnaseq.gene.kallisto@assayData$exprs)

[ttdtrang]

Could you please clarify on the error messages you got and at what step?

[maxbox63]

Sure:

Restarting R session...

if (!require("BiocManager", quietly = TRUE))

• install.packages("BiocManager")
  

Bioconductor version 3.10 (BiocManager 1.30.16), R 3.6.3 (2020-02-29)
Bioconductor version '3.10' is out-of-date; the current release version '3.14' is available
with R version '4.1'; see https://bioconductor.org/install

BiocManager::install("edgeR")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.10 (BiocManager 1.30.16), R 3.6.3 (2020-02-29)
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages: rpart
path: /usr/lib/R/site-library
packages: brew, mapproj, mockery, sessioninfo, sodium
path: /usr/local/lib/R/site-library
packages: evaluate, irlba, yaml
Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install:
'edgeR'

devtools::install_github('ttdtrang/data-rnaseq-sarcoma')
Downloading GitHub repo ttdtrang/data-rnaseq-sarcoma@HEAD
✓ checking for file ‘/tmp/RtmpTm7OjF/remotes25f8a15cd3222/ttdtrang-data-rnaseq-sarcoma-4c0d406/DESCRIPTION’ ...
─ preparing ‘data.rnaseq.sarcoma’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘data.rnaseq.sarcoma_0.0.0.9000.tar.gz’
Installing package into ‘/home/maxr/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified)

• installing source package ‘data.rnaseq.sarcoma’ ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  Warning: file ‘sarcoma.rnaseq.gene.kallisto.rda’ has magic number 'versi'
  Use of save versions prior to 2 is deprecated
  Error in load(zfile, envir = tmp_env) :
  bad restore file magic number (file may be corrupted) -- no data loaded
  ERROR: lazydata failed for package ‘data.rnaseq.sarcoma’
• removing ‘/home/maxr/R/x86_64-pc-linux-gnu-library/3.6/data.rnaseq.sarcoma’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpTm7OjF/file25f8a34e63d82/data.rnaseq.sarcoma_0.0.0.9000.tar.gz’ had non-zero exit status

[ttdtrang]

So the error is coming from devtools::install_github() not supporting downloading LFS files automatically (r-lib/devtools#889). This would be resolved by these steps:

1. Installing Git LFS
2. Clone the repo locally and install using devtools::install().

[ttdtrang]

It turns out my free LFS account also ran out of quota/bandwidth. I'll need to find some alternative storage for those data files.

[maxbox63]

Thanks for your responses. I was unaware of Git LFS, but now it sounds as if I don't need to install it yet. I have been able to use the lymphoma set, and the sarcoma set was the second I tried. I will try the rest while you decide how to store the files.

Regards, Max