Problems with Report #3
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I just updated my own system (same R version, also Catalina) and can still generate the reports. Could you please post your sessionInfo() after running runMicrobiomeExplorer()? Thank you! |
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Hi Janina,
Thank you very much for your time and help. I don’t know if I understood you exactly but I tried (im very new with bioinformatics). I loaded microbiomeExplorer (library) on R and then I used "session_info(pkgs=NULL include_base=FALSE)” I got this:
session_info(pkgs = NULL, include_base = FALSE)
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.3 (2020-10-10)
os macOS High Sierra 10.13.6
system x86_64, darwin17.0
ui AQUA
language (EN)
collate es_ES.UTF-8
ctype es_ES.UTF-8
tz Europe/Madrid
date 2021-01-15
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
Biobase * 2.50.0 2020-10-27 [1] Bioconductor
BiocGenerics * 0.36.0 2020-10-27 [1] Bioconductor
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.2)
caTools 1.18.0 2020-01-17 [1] CRAN (R 4.0.2)
cli 2.2.0 2020-11-20 [1] CRAN (R 4.0.2)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.0.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.2)
foreach 1.5.1 2020-10-15 [1] CRAN (R 4.0.2)
glmnet * 4.0-2 2020-06-16 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
gplots 3.1.1 2020-11-28 [1] CRAN (R 4.0.2)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.2)
htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2)
iterators 1.0.13 2020-10-15 [1] CRAN (R 4.0.2)
KernSmooth 2.23-18 2020-10-29 [1] CRAN (R 4.0.2)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.3)
limma * 3.46.0 2020-10-27 [1] Bioconductor
locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.0.2)
magrittr * 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
Matrix * 1.3-2 2021-01-06 [1] CRAN (R 4.0.2)
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.2)
metagenomeSeq * 1.32.0 2020-10-27 [1] Bioconductor
microbiomeExplorer * 1.0.4 2021-01-11 [1] Github (zoecastillo/microbiomeExplorer@e29de49)
mime 0.9 2020-02-04 [1] CRAN (R 4.0.2)
promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
RColorBrewer * 1.1-2 2014-12-07 [1] CRAN (R 4.0.2)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.2)
sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
shape 1.4.5 2020-09-13 [1] CRAN (R 4.0.2)
shiny * 1.5.0 2020-06-23 [1] CRAN (R 4.0.2)
shinydashboard 0.7.1 2018-10-17 [1] CRAN (R 4.0.2)
survival 3.2-7 2020-09-28 [1] CRAN (R 4.0.3)
withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)
Wrench 1.8.0 2020-10-28 [1] Bioconductor
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2)
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
I tried also session info after running runMicrobiomeExplorer() but R doesn’t return any info, I don’t know if this is the info required (I hope yes). Reading the report I see I was wrong and my macOs version is High Sierra, I work in remote with a server which works with macOs catalina (my bad) and before to install the packages on the server first I work local on my computer thats the reason of the mistake.
I hope it helps, once more thank you for your help.
Regards
Antonio
… El 14 ene 2021, a las 23:36, Janina Reeder ***@***.***> escribió:
I just updated my own system (same R version, also Catalina) and can still generate the reports.
So, it's not related to the R version or OS.
Could you please post your sessionInfo() after running runMicrobiomeExplorer()?
It looks like the knitting or rendering step is not starting properly, but I don't know why. I had someone else report a similar issue from a windows environment.
Thank you!
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Thank you! Could you please try loading the knitr and rmarkdown packages explicitly before running runMicrobiomeExplorer()? Another thing you could try is to look at the temp folder shown in the error reported after you attempt to generate the report while the application is still running. (above it is "/var/folders/sy/4mzmjcq17txbv3vnznqk2v5c0000gn/T//RtmpHv8asR", but this will be different every time you run the app). If that works, can you see any me_report.* files in there? Best, Janina |
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Hi Janina
I loaded knit (v 1.30) and rmarkdown (v 2.6) but same error:
…-- Sending report to /var/folders/sr/2r58hx090yx8qzmvzv3zsk2m0000gp/T//Rtmpnz0ZsM --
-- Removing /var/folders/sr/2r58hx090yx8qzmvzv3zsk2m0000gp/T//Rtmpnz0ZsM/me_report.Rmd--
-- entering my report generator --
-- creating header --
-- setting toc ----- data processing ----- header created! --
-- build intro text --
-- merged code --
gen report try value: try-error
Any suggestion?
Best wishes
El 15 ene 2021, a las 16:11, Janina Reeder ***@***.***> escribió:
Thank you!
Could you please try loading the knitr and rmarkdown packages explicitly before running runMicrobiomeExplorer()?
Those contain the functions we call to generate the reports, so it would be good to see which versions those are.
Another thing you could try is to look at the temp folder shown in the error reported after you attempt to generate the report while the application is still running. (above it is "/var/folders/sy/4mzmjcq17txbv3vnznqk2v5c0000gn/T//RtmpHv8asR", but this will be different every time you run the app). If that works, can you see any me_report.* files in there?
Best,
Janina
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Hi Janina,
I have installed microbiomeExplorer in the server (macOS Catalina and R 4.0.3) and I get same error (I also tried to load first knitr and rmarkdown as you told me). Please find attached me_report if it helps.
Regards
… El 15 ene 2021, a las 16:11, Janina Reeder ***@***.***> escribió:
Thank you!
Could you please try loading the knitr and rmarkdown packages explicitly before running runMicrobiomeExplorer()?
Those contain the functions we call to generate the reports, so it would be good to see which versions those are.
Another thing you could try is to look at the temp folder shown in the error reported after you attempt to generate the report while the application is still running. (above it is "/var/folders/sy/4mzmjcq17txbv3vnznqk2v5c0000gn/T//RtmpHv8asR", but this will be different every time you run the app). If that works, can you see any me_report.* files in there?
Best,
Janina
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Thank you, Those are the same versions my system uses. I will have to do some more testing to see if I can figure out what causes the problem. The only other thing I could think about right now would be pandoc, but if you can run knit markdown documents, it should be there (I think). But just in case, could you please check if pandoc is installed and findable in your system. If it is, I will have to get back to you. |
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Hi Janina,
Now its working!! :) I had to solve some more errors, if it helps I did:
Install phantomjs on R —> webshot::install_phantomjs()
Then on terminal throw brew install basictex and throw pip install pandoc
Thank you for your help
Best wishes
A. Galiana
… El 20 ene 2021, a las 4:44, Janina Reeder ***@***.***> escribió:
Thank you,
Those are the same versions my system uses. I will have to do some more testing to see if I can figure out what causes the problem. The only other thing I could think about right now would be pandoc, but if you can run knit markdown documents, it should be there (I think). But just in case, could you please check if pandoc is installed and findable in your system.
If it is, I will have to get back to you.
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Thank you very much for sharing this! I am very glad you were able to figure out the problem. |
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Hi!
Im trying to get the report and I get this error:
Listening on http://127.0.0.1:4554
-- Sending report to /var/folders/sy/4mzmjcq17txbv3vnznqk2v5c0000gn/T//RtmpHv8asR --
-- Removing /var/folders/sy/4mzmjcq17txbv3vnznqk2v5c0000gn/T//RtmpHv8asR/me_report.Rmd--
-- entering my report generator --
-- creating header --
-- setting toc ----- data processing ----- header created! --
-- build intro text --
-- merged code --
gen report try value: try-error
Im using R version 4.0.3 on macOs Catalina.
Any suggestion?
Best wishes!
A. Galiana
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