Error: stack file is corrupt

cz0430 commented 1 year ago

Hi, I tried to use openprimer and installed all external tools, when I run the script in conda env under centOS system, I got the below error msg:

library(openPrimeR) Error: stack file is corrupt Error: stack file is corrupt There are missing/non-functioning external tools. To use the full potential of openPrimeR, please make sure that the required versions of the speciied tools are

            installed and that they are functional:

o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/) o OligoArrayAux (http://unafold.rna.albany.edu/OligoArrayAux.php) o Pandoc (http://pandoc.org) The number of cores for was set to '2' by 'parallel_setup()'. Warning messages: 1: In check.tool.function() : oligoArrayAux failed checks: disabled. Do you have the UNAFOLDDAT environment variable set? 2: In check.tool.function() : oligoArrayAux failed checks: disabled. Do you have the UNAFOLDDAT environment variable set? 3: In fun(libname, pkgname) : 'Pandoc' is non-functional, since 'pdflatex' is not installed on your system.

How can I fix such problems?Thanks a lot!

matdoering commented 1 year ago

Maybe have a look here? https://support.bioconductor.org/p/9139543/

cz0430 commented 1 year ago

Thanks a lot for reply. I have solved the above issue by reinstalling oligoarrayaux. However, when I ran the script provided on the HTML link get from bioconductor. I got the following error at the create_report step:

create_report(constraint.df, template.df, my.file,

settings, sample.name = "My analysis")

kpathsea: Running mktexfmt pdftex.fmt Can't locate mktexlsr.pl in @INC (@INC contains: /public/home/miniconda3/envs/openprimer2/share/texlive/tlpkg /public/home/miniconda3/envs/openprimer2/share/texlive/texmf-dist/scripts/texlive /public/home/miniconda3/envs/openprimer2/lib/perl5/5.32/site_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/site_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/5.32/vendor_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/vendor_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/5.32/core_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/core_perl .) at /public/home/miniconda3/envs/openprimer2/bin/mktexfmt line 23. BEGIN failed--compilation aborted at /public/home/miniconda3/envs/openprimer2/bin/mktexfmt line 25. !!! Error: pdfTeX run failed with value 1!

kpathsea: Running mktexfmt pdftex.fmt Can't locate mktexlsr.pl in @INC (@INC contains: /public/home/miniconda3/envs/openprimer2/share/texlive/tlpkg /public/home/miniconda3/envs/openprimer2/share/texlive/texmf-dist/scripts/texlive /public/home/miniconda3/envs/openprimer2/lib/perl5/5.32/site_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/site_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/5.32/vendor_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/vendor_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/5.32/core_perl /public/home/miniconda3/envs/openprimer2/lib/perl5/core_perl .) at /public/home/miniconda3/envs/openprimer2/bin/mktexfmt line 23. BEGIN failed--compilation aborted at /public/home/miniconda3/envs/openprimer2/bin/mktexfmt line 25. !!! Error: pdfTeX run failed with value 1! [WARNING] Deprecated: --self-contained. use --embed-resources --standalone tlmgr: package repository https://ctan.math.illinois.edu/systems/texlive/tlnet (verified) [1/1, ??:??/??:??] install: wallpaper [2k] running mktexlsr ... done running mktexlsr. tlmgr: package log updated: /public/home/.TinyTeX/texmf-var/web2c/tlmgr.log tlmgr: command log updated: /public/home/.TinyTeX/texmf-var/web2c/tlmgr-commands.log tlmgr: package repository https://ctan.math.illinois.edu/systems/texlive/tlnet (verified) [1/1, ??:??/??:??] install: eso-pic [4k] running mktexlsr ... done running mktexlsr. tlmgr: package log updated: /public/home/.TinyTeX/texmf-var/web2c/tlmgr.log tlmgr: command log updated: /public/home/.TinyTeX/texmf-var/web2c/tlmgr-commands.log tlmgr: package repository https://ctan.math.illinois.edu/systems/texlive/tlnet (verified) [1/1, ??:??/??:??] install: caption [60k] running mktexlsr ... done running mktexlsr. tlmgr: package log updated: /public/home/.TinyTeX/texmf-var/web2c/tlmgr.log tlmgr: command log updated: /public/home/.TinyTeX/texmf-var/web2c/tlmgr-commands.log ! LaTeX Error: Unicode character 五 (U+4E94) not set up for use with LaTeX.

Error : LaTeX failed to compile /tmp/RtmpTfM4HG/file31f19250ee1b1.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See file31f19250ee1b1.log for more info.外: Warning messages: 1: In matrix(c(my.ok, my.fail, ref.ok, ref.fail), nrow = 2, ncol = 2, : data length differs from size of matrix: [22 != 2 x 2] 2: guides(<scale> = FALSE) is deprecated. Please use guides(<scale> = "none") instead. NULL Warning message: In render_report(params, "report.Rmd", fname) : No PDF file was produced, please check the console output and whether all Latex dependencies are installed (Texlive available?).

Rscript -e 'tinytex::install_tinytex();rmarkdown::render("QuantDataProcessingScript.Rmd")' Error: unexpected string constant在"Rscript -e 'tinytex::install_tinytex();rmarkdown::render("QuantDataProcessingScript.Rmd")'"

It seems a pdfLatex problem, so I installed r-tinytex, the same error still showed up. May I know how i can solve it?thanks a lot!

matdoering commented 1 year ago

Seems you need to fix your Latex install on your machine. Since this is out-of-scope of the package, I will close this one.

matdoering / openPrimeR

Error: stack file is corrupt #14