Installing and problem with : package 'Rhtslib'

Britta

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Aug 1, 2018, 6:32:40 AM8/1/18

to methylkit_discussion

Dear all, Dear Altuna,

I have problems installing the package Methylkit on my new local computer.

I get this message after downloading from the GitHub: Error: package 'Rhtslib' 1.12.1 was found, but >= 1.13.1 is required by 'al2na-methylKit-75b949f'

However also later when re-installing Rhtslib I get another error (see below).

Can you help me? or shall I write Rhtslib-people? or is it something really easy I just don't see?

Best wishes and thanks a lot,

Britta

> library(devtools)

> install_github("al2na/methylKit", build_vignettes=FALSE,

+ repos=BiocInstaller::biocinstallRepos(),

+ dependencies=TRUE,type="source")

Using GitHub PAT from envvar GITHUB_PAT

Downloading GitHub repo al2na/methylKit@master

from URL https://api.github.com/repos/al2na/methylKit/zipball/master

Installing methylKit

'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \

'/private/var/folders/27/h99dl6wn73n43cw31xdmb75h0000gp/T/Rtmp4MvTe0/devtools13437fc47ef2/al2na-methylKit-75b949f' \

--library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests

During startup - Warning messages:

1: Setting LC_CTYPE failed, using "C"

2: Setting LC_TIME failed, using "C"

3: Setting LC_MESSAGES failed, using "C"

4: Setting LC_MONETARY failed, using "C"

* installing *source* package 'methylKit' ...

** libs

Error: package 'Rhtslib' 1.12.1 was found, but >= 1.13.1 is required by 'al2na-methylKit-75b949f'

* removing '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/methylKit'

Installation failed: Command failed (1)

> library(devtools)

> install_github("al2na/methylKit", build_vignettes=FALSE,

+ repos=BiocInstaller::biocinstallRepos(),ref="development",

+ dependencies=TRUE)

> library(Rhtslib)

Rhtslib htslib version 1.7

Than I try to update the htslib package - but another command fails....

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

Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help

> biocLite("Rhtslib",type="source")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).

Installing package(s) 'Rhtslib'

trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/Rhtslib_1.12.1.tar.gz'

Content type 'application/x-gzip' length 1424650 bytes (1.4 MB)

==================================================

downloaded 1.4 MB

During startup - Warning messages:

1: Setting LC_CTYPE failed, using "C"

2: Setting LC_TIME failed, using "C"

3: Setting LC_MESSAGES failed, using "C"

4: Setting LC_MONETARY failed, using "C"

* installing *source* package 'Rhtslib' ...

** libs

cd "htslib-1.7" && make -f "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f "Makefile.Rhtslib"

Makefile.Rhtslib:128: warning: overriding commands for target `.c.o'

/Library/Frameworks/R.framework/Resources/etc/Makeconf:159: warning: ignoring old commands for target `.c.o'

clang -g -Wall -O2 -I. -c -o kfunc.o kfunc.c

clang -g -Wall -O2 -I. -c -o knetfile.o knetfile.c

clang -g -Wall -O2 -I. -c -o kstring.o kstring.c

clang -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c

clang -g -Wall -O2 -I. -c -o bgzf.o bgzf.c

clang -g -Wall -O2 -I. -c -o errmod.o errmod.c

clang -g -Wall -O2 -I. -c -o faidx.o faidx.c

clang -g -Wall -O2 -I. -c -o hfile.o hfile.c

clang -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c

echo '#define HTS_VERSION "1.7"' > version.h

clang -g -Wall -O2 -I. -c -o hts.o hts.c

clang -g -Wall -O2 -I. -c -o hts_os.o hts_os.c

clang -g -Wall -O2 -I. -c -o md5.o md5.c

clang -g -Wall -O2 -I. -c -o multipart.o multipart.c

clang -g -Wall -O2 -I. -c -o probaln.o probaln.c

clang -g -Wall -O2 -I. -c -o realn.o realn.c

clang -g -Wall -O2 -I. -c -o regidx.o regidx.c

clang -g -Wall -O2 -I. -c -o sam.o sam.c

clang -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c

clang -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c

clang -g -Wall -O2 -I. -c -o tbx.o tbx.c

clang -g -Wall -O2 -I. -c -o textutils.o textutils.c

clang -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c

clang -g -Wall -O2 -I. -c -o vcf.o vcf.c

clang -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c

clang -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c

clang -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c

clang -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c

clang -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c

clang -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c

clang -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c

cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found

#include <lzma.h>

^~~~~~~~

1 error generated.

make[1]: *** [cram/cram_io.o] Error 1

make: *** [htslib] Error 2

ERROR: compilation failed for package 'Rhtslib'

* removing '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib'

* restoring previous '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib'

> session_info()

Session info -------------------------------------------------------------------------------------------------------------------------

setting value

version R version 3.5.0 (2018-04-23)

system x86_64, darwin15.6.0

ui RStudio (1.1.447)

language (EN)

collate C

tz Europe/Berlin

date 2018-08-01

Packages -----------------------------------------------------------------------------------------------------------------------------

package * version date source

base * 3.5.0 2018-04-24 local

BiocInstaller * 1.30.0 2018-05-01 Bioconductor

compiler 3.5.0 2018-04-24 local

curl 3.2 2018-03-28 CRAN (R 3.5.0)

datasets * 3.5.0 2018-04-24 local

devtools * 1.13.6 2018-06-27 CRAN (R 3.5.0)

digest 0.6.15 2018-01-28 CRAN (R 3.5.0)

git2r 0.23.0 2018-07-17 CRAN (R 3.5.0)

graphics * 3.5.0 2018-04-24 local

grDevices * 3.5.0 2018-04-24 local

httr 1.3.1 2017-08-20 CRAN (R 3.5.0)

knitr 1.20 2018-02-20 CRAN (R 3.5.0)

memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)

methods * 3.5.0 2018-04-24 local

R6 2.2.2 2017-06-17 CRAN (R 3.5.0)

Rhtslib * 1.12.1 2018-05-31 Bioconductor

stats * 3.5.0 2018-04-24 local

tools 3.5.0 2018-04-24 local

utils * 3.5.0 2018-04-24 local

withr 2.1.2 2018-03-15 CRAN (R 3.5.0)

yaml 2.2.0 2018-07-25 CRAN (R 3.5.0)

zlibbioc 1.26.0 2018-05-01 Bioconductor

>

Britta

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Aug 1, 2018, 8:05:36 AM8/1/18

to methylkit_discussion

new info: I actually get the exact same error using Linux_Gnu Rstudio (1.1.453) Revision 3.51

Johan Zicola

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Aug 1, 2018, 9:19:41 AM8/1/18

to methylkit_discussion

Dear Britta,

I was struggling as well for methylKit installation with both Windows and Linux because of Rhtslib. Here how I solved the problem for the two OS. In both case, the solution is to install manually the 'misnamed' last version of Rhtslib:

For Linux
I downloaded the version Rhtslib_1.13.4.tar.gz https://www.bioconductor.org/packages/devel/bioc/html/Rhtslib.html
and put it in the library directory, enter command in bash

R CMD INSTALL Rhtslib_1.13.4.tar.gz

Ignore the fact that the name of the archive is Rhtslib_1.13.4.tar.gz, it is actually 1.7, as you will see.
Go in R 3.5.0

library(Rhtslib)
Rhtslib htslib version 1.7


library(devtools)
install_github("al2na/methylKit", build_vignettes=FALSE,

 
  repos=BiocInstaller::biocinstallRepos(),
  dependencies=TRUE)
library(methylKit)

For Windows
Download the binary zip from https://www.bioconductor.org/packages/devel/bioc/html/Rhtslib.html
In R 3.5.0, type:

# Give path to the zip file
install.packages('C:/Users/zicola/Documents/R/win-library/3.5/Rhtslib_1.13.4.zip', lib='C:/Users/zicola/Documents/R/win-library/3.5/',repos = NULL)



library(Rhtslib)
Rhtslib htslib version 1.7

Install Methylkit


library(devtools)
install_github("al2na/methylKit", build_vignettes=FALSE,

 
   repos=BiocInstaller::biocinstallRepos(),
   dependencies=TRUE)

library(methylKit)
# Works!

Britta

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Aug 1, 2018, 12:12:43 PM8/1/18

to methylkit_discussion

Dear Johan,

thanks a lot! You gave me the right idea to download the right package version.

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("Rhtslib", version = "devel")

And than

install_github("al2na/methylKit", build_vignettes=FALSE,

+ repos=BiocInstaller::biocinstallRepos(),ref="development",

+ dependencies=TRUE)

This finally worked... (only) on the linux.

Thanks again!

Johan Zicola

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Aug 2, 2018, 3:29:06 AM8/2/18

to methylkit_discussion

Dear Britta,

I remember now that I also had a Rtools problem in Windows, which could also be your case. You can give a try and install the last Rtools (version 35) if not done already (download on https://cran.r-project.org/bin/windows/Rtools/ and launch the executable). Tip the "Add rtools to system PATH during installation" (see this helpful thread https://stackoverflow.com/questions/50034966/no-rtools-compatible-with-r-version-3-5-0-was-found).
Reopen R

> library(devtools)


> install_github("al2na/methylKit", build_vignettes=FALSE, 
+   repos=BiocInstaller::biocinstallRepos(),

+   dependencies=TRUE)

library(methylKit)

Let me know if this solve your Windows problem as well.
Cheers,

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