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Here are the steps I use to build |
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Answered by
martin-g
Sep 22, 2023
Replies: 2 comments 31 replies
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l use bioconda-utils to build |
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20 replies
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CentOS 8 (8.4.2105) has it for |
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I've found the symbol in but the following patch still fails the same: diff --git i/recipes/bioconductor-msa/build.sh w/recipes/bioconductor-msa/build.sh
index c1d13421f5..0be3f8bcc5 100644
--- i/recipes/bioconductor-msa/build.sh
+++ w/recipes/bioconductor-msa/build.sh
@@ -4,8 +4,9 @@ grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
mkdir -p ~/.R
echo -e "CC=$CC
FC=$FC
-CXX=$CXX
-CXX98=$CXX
-CXX11=$CXX
-CXX14=$CXX" > ~/.R/Makevars
-$R CMD INSTALL --build .
\ No newline at end of file
+CXX=$CXX -lpthread_nonshared
+CXX98=$CXX -lpthread_nonshared
+CXX11=$CXX -lpthread_nonshared
+CXX14=$CXX -lpthread_nonshared" > ~/.R/Makevars
+sudo yum install -y glibc-devel
+$R CMD INSTALL --build . |
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lt's very cool, but l'm a little confused. ls this because aarch64 lacks some important symbols? |
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It looks to me as a packaging problem in CentOS 7 (not maintained since a long time!). |
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Finally I have a successful build! diff --git i/recipes/bioconductor-biocgenerics/meta.yaml w/recipes/bioconductor-biocgenerics/meta.yaml
index 785b193559..6e40c129df 100644
--- i/recipes/bioconductor-biocgenerics/meta.yaml
+++ w/recipes/bioconductor-biocgenerics/meta.yaml
@@ -4,7 +4,7 @@
package:
name: 'bioconductor-{{ name|lower }}'
- version: '{{ version }}'
+ version: '{{ version }}.1'
source:
url:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
diff --git i/recipes/bioconductor-genomeinfodb/meta.yaml w/recipes/bioconductor-genomeinfodb/meta.yaml
index 7cbd5ae154..5d946ce12b 100644
--- i/recipes/bioconductor-genomeinfodb/meta.yaml
+++ w/recipes/bioconductor-genomeinfodb/meta.yaml
@@ -4,7 +4,7 @@
package:
name: 'bioconductor-{{ name|lower }}'
- version: '{{ version }}'
+ version: '{{ version }}.1'
source:
url:
- 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
diff --git i/recipes/bioconductor-msa/build.sh w/recipes/bioconductor-msa/build.sh
index c1d13421f5..1f2bd99a69 100644
--- i/recipes/bioconductor-msa/build.sh
+++ w/recipes/bioconductor-msa/build.sh
@@ -1,4 +1,5 @@
#!/bin/bash
+set -x
mv DESCRIPTION DESCRIPTION.old
grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
mkdir -p ~/.R
@@ -8,4 +9,7 @@ CXX=$CXX
CXX98=$CXX
CXX11=$CXX
CXX14=$CXX" > ~/.R/Makevars
-$R CMD INSTALL --build .
\ No newline at end of file
+sudo yum install -y glibc-devel
+echo -e '\nPKG_LIBS=-Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a -Wl,--no-whole-archive -lpthread_nonshared -lpthread' >> ./src/Makevars
+cat ./src/Makevars
+$R CMD INSTALL --build . |
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That's cool, l've built it successfully. l want to know why, could you ask the principle of this? |
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11 replies
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See https://github.com/UBod/msa/blob/33868780db208908d9dbbac04a626e05fb31d4e1/src/Makevars#L1 With I just set the same linker options as the original ones and added |
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Answer selected by
martin-g
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Cool, the process is very rigorous, let me study seriously, can you help me take time to look at the other questions? Thanks |
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Which other questions ? |
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when l build r-nbpseq, the following error occurred. ls the error related to bioconductor-msa? @martin-g Could you help to take a look, thanks. |
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I started using |
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See https://github.com/UBod/msa/blob/33868780db208908d9dbbac04a626e05fb31d4e1/src/Makevars#L1
Here the logic sets the special
PKG_LIBSenvironment variable that is used by R to add the linker options, see https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Using-Makevars:With
I just set the same linker options as the original ones and added
-lpthread. This way CentOS 7 aarch64 also adds thelibpthreadlib…