Installation error

Question

Installation error

davisidarta opened this issue 5 years ago · comments

Hello there BiocSingular Team!

I'm trying to install batchelor. However, when I run devtools::install_github("LTLA/batchelor"), I get the following error output:


Downloading GitHub repo LTLA/batchelor@master
Skipping 2 packages not available: BiocNeighbors, BiocSingular
Skipping 11 packages ahead of CRAN: beachmat, BiocGenerics, BiocParallel, DelayedArray, gtable, HDF5Array, IRanges, rhdf5, Rhdf5lib, rlang, S4Vectors
Installing 17 packages: Biobase, BiocSingular, DelayedMatrixStats, edgeR, GenomeInfoDb, GenomeInfoDbData, GenomicRanges, limma, locfit, rjson, scater, shinydashboard, SingleCellExperiment, SummarizedExperiment, tximport, XVector, zlibbioc
Installing packages into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Error: (converted from warning) package ‘BiocSingular’ is not available (for R version 3.5.3)

I've then tried to install biocSingular. However, I get the following error:

In file included from /usr/local/lib/R/site-library/beachmat/include/beachmat/all_readers.h:4:0,
                 from /usr/local/lib/R/site-library/beachmat/include/beachmat/LIN_matrix.h:4,
                 from /usr/local/lib/R/site-library/beachmat/include/beachmat/numeric_matrix.h:4,
                 from compute_scale.cpp:2:
/usr/local/lib/R/site-library/beachmat/include/beachmat/beachmat.h:15:19: fatal error: H5Cpp.h: No such file or directory
 #include "H5Cpp.h"
                   ^
compilation terminated.
/usr/local/lib/R/etc/Makeconf:172: recipe for target 'compute_scale.o' failed
make: *** [compute_scale.o] Error 1
ERROR: compilation failed for package ‘BiocSingular’
* removing ‘/usr/local/lib/R/site-library/BiocSingular’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/tmp/RtmpGJQkfa/file1977a4d39ec/BiocSingular_0.99.14.tar.gz’ had non-zero exit status

Does anyone know a way to solve this? Any help will be really appreciated.

Thanks in advance!

Davi

Aaron Lun · Answer 1 · Mon Apr 01 2019 04:42:20 GMT+0800 (China Standard Time)

Install BiocSingular as per the instructions on the Bioconductor landing page.

https://bioconductor.org/packages/devel/bioc/html/BiocSingular.html

It is worth keeping in mind that the Github repository is purely for the convenience of the developers. The canonical form of the package is always on Bioconductor, as noted in the description for this repository.

Davi Sidarta · Answer 2 · Mon Apr 01 2019 04:51:47 GMT+0800 (China Standard Time)

I've done that as well. There's an error message output:

Error: Bioconductor version '3.9' requires R version '3.6'; see https://bioconductor.org/install

However, R last build is 3.5.3. (https://cran.r-project.org/bin/windows/base/). How is someone supposed to install an unreleased build?

I'm very sorry if this is too basic. I've worked with bioinformatics for several months now, but it's my first time with BiocSingular.

Thank you in advance!

Best,

Davi

Aaron Lun · Answer 3 · Mon Apr 01 2019 10:25:14 GMT+0800 (China Standard Time)

https://www.r-project.org/, "Planting of a Tree".

Aaron Lun · Answer 4 · Thu Apr 18 2019 12:29:43 GMT+0800 (China Standard Time)

I'm going to assume this got fixed somewhere along the line.

Zhuoer Dong · Answer 5 · Mon May 06 2019 09:03:44 GMT+0800 (China Standard Time)

still the same compilation error for remotes::install_bioc('release/BiocSingular')

Aaron Lun · Answer 6 · Mon May 06 2019 09:04:23 GMT+0800 (China Standard Time)

Session info?

Zhuoer Dong · Answer 7 · Mon May 06 2019 15:32:41 GMT+0800 (China Standard Time)

Later I find that BiocManager::install('BiocSingular') succeeds, because it uses beachmat 2.0.0, while the former uses beachmat 1.4.0.

Zhuoer Dong · Answer 8 · Mon May 06 2019 17:16:56 GMT+0800 (China Standard Time)

I think it's an issue of remotes package, and I will report there. Thank you anyway!