ShortRead Installation in R 4.2.0 and zlib library
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Bogdan ▴ 670
@bogdan-2367
Last seen 9 months ago
Palo Alto, CA, USA

Dear all,

I am encountering an unusual situation when I am installing ShortRead in R.4.2.0.

<> I have been installing ShortRead in many ways, via 1) BiocManager::install, 2) from a github repo, 3) via conda (bioconductor-shortread).

In the cases 1) and 2), there is a compilation error that has been reported before

checking for gzeof in -lz... no
configure: error: zlib not found

in the case 3) conflicts between packages have been found.

<> I have been installing zlib in several ways, from source code, via conda (conda install -c conda-forge zlib), or by installing the libraries :

sudo apt-get install zlibc zlib1g zlib1g-dev

After installing zlib, the message that I am given after I type BiocManager::install(ShortReads) is the same as above :

checking for gzeof in -lz... no
configure: error: zlib not found

Is there anything else that I shall do in order to find a solution ? Any help is very much appreciated ! Thank you !

ps : I have read the previous comments on the support site related to "zlib not found" error, unfortunately the proposed solutions did not work for me.

I am running R on an aws instance of Ubuntu 20.04, and the R version is :

> R.Version()
$platform
[1] "x86_64-conda-linux-gnu"

$arch
[1] "x86_64"

$os
[1] "linux-gnu"

$system
[1] "x86_64, linux-gnu"

$status
[1] ""

$major
[1] "4"

$minor
[1] "2.0"

$year
[1] "2022"

$month
[1] "04"

$day
[1] "22"

$`svn rev`
[1] "82229"

$language
[1] "R"

$version.string
[1] "R version 4.2.0 (2022-04-22)"

$nickname
[1] "Vigorous Calisthenics"
R-4 ShortRead • 1.5k views
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Entering edit mode

How did you install R? It looks like with conda.

I don't really know how to debug the conda installation. I'd guess the error was not necessarily saying that zlib could not be found, but that the version found (e.g., the one available on the system or installed through apt get...) was not consistent with the compiler being used (through conda). So can you install ShortRead with conda (not zlib per se)? The top of this comment Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH has an example that was reproducible at the time.

Personally, I would install R natively (both r-base and r-base-dev) following these instructions https://cloud.r-project.org/bin/linux/ubuntu/fullREADME.html. And if necessary I'd use apt to install zlib1g-dev

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Hi Martin, thank you very much for your reply, especially during the weekend ! Very much appreciated !

I guess that the cause of the error may have been caused by the settings of AWS EC2 that I have been using.

I have switched to the BioC docker containers, and it works very well ! Thank you for making those available !

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@martin-morgan-1513
Last seen 3 days ago
United States

I'll transfer the comments to an answer.

The best guess is that the problem arises from mixing (bio)conda and BiocManager ('native') to install packages.

Workarounds include

  • Use Bioconductor docker images rather than conda for containerized installation
  • Only use (bio)conda for package installation
  • Do not use (bio)conda for R, instead install from R 'natively' and use BiocManager to install all packages.

It would also be useful, though challenging, to

  • Figure out the source of the problem, and provide an upstream (bioconda) fix

This previous support site issue provides many avenues for exploration if one is committed to combining conda and native installations.

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