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LTLA / BiocSingular

Clone of the Bioconductor repository for the BiocSingular package.
https://bioconductor.org/packages/devel/bioc/html/BiocSingular.html
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Installation error #4

Closed davisidarta closed 5 years ago

davisidarta commented 5 years ago

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

LTLA commented 5 years ago

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.

davisidarta commented 5 years ago

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

LTLA commented 5 years ago

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

LTLA commented 5 years ago

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

dongzhuoer commented 5 years ago

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

LTLA commented 5 years ago

Session info?

dongzhuoer commented 5 years ago

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

dongzhuoer commented 5 years ago

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