Re: [Bioc-devel] ptime ERROR
This is the error, sorry my hand slipped when writing the last email. Thank you.
http://bioconductor.org/checkResults/devel/bioc-LATEST/M3C/malbec2-checksrc.html
checking examples ... ERROR
Running examples in ‘M3C-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
On Thu, 6 Feb 2020 at 16:07, Christopher John
wrote:
> Hi
>
> I was wondering will this error disappear by itself? Because I did not
> change the package.
>
> Thanks,
>
> Chris
>
>
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[Bioc-devel] ptime ERROR
Hi I was wondering will this error disappear by itself? Because I did not change the package. Thanks, Chris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Windows only vignette error - any ideas?
Hi Since this morning I am getting an error for the Windows build only of my M3C package, shown below. Could anyone help please? Thanks, Chris * checking for file 'M3C/DESCRIPTION' ... OK * preparing 'M3C': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'M3Cvignette.Rmd' using rmarkdown ! Package ifvtex Error: Name clash, \ifvtex is already defined. Error: processing vignette 'M3Cvignette.Rmd' failed with diagnostics: Failed to compile M3Cvignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See M3Cvignette.log for more info. --- failed re-building 'M3Cvignette.Rmd' SUMMARY: processing the following file failed: 'M3Cvignette.Rmd' Error: Vignette re-building failed. Execution halted [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] New error appeared on dev without updating the development version
Hi I haven't done an update in a while, but got the following error message like yesterday just on windows, any ideas? Seems vignette related. Thanks. Chris ## ## ### ### Running command: ### ### chmod a+r M3C -R && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data M3C ### ## ## * checking for file 'M3C/DESCRIPTION' ... OK * preparing 'M3C': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'M3Cvignette.Rmd' using rmarkdown Loading required package: pkgmaker Loading required package: registry Attaching package: 'pkgmaker' The following object is masked from 'package:base': isFALSE Loading required package: rngtools Loading required package: cluster NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 39/40 Attaching package: 'gplots' The following object is masked from 'package:stats': lowess ***PCA wrapper function*** running... done. ***M3C*** method: Monte Carlo simulation clustering algorithm: pam annotation: yes running simulations... done. running consensus cluster algorithm for real data... done. running clinical analysis type: chi optimal K: 4 PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek. ==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-7-1.pdf'. PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek. ==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-8-1.pdf'. ***PCA wrapper function*** running... done. ***t-SNE wrapper function*** running... done. ***M3C*** method: penalised stability clustering algorithm: pam annotation: none running consensus cluster algorithm for real data... done. optimal K: 5 PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek. ==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-10-1.pdf'. PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek. ==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-10-2.pdf'. PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek. ==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-10-3.pdf'. ***clustersim*** computing simulated data using linear combination... calculating PCs of data and performing kmeans... computing centroids of clusters and pulling apart... transforming pulled apart PC co ordinates back to dataset... finished. PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek. ==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-11-1.pdf'. ! Package ifvtex Error: Name clash, \ifvtex is already defined. Error: processing vignette 'M3Cvignette.Rmd' failed with diagnostics: Failed to compile M3Cvignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See M3Cvignette.log for more info. --- failed re-building 'M3Cvignette.Rmd' SUMMARY: processing the following file failed: 'M3Cvignette.Rmd' Error: Vignette re-building failed. Execution halted [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Version number error
Still stuck here trying to update. I think I may have been a bit special with my version numbering. Well let me know if there is a solution or do I just wait until the next release..(?) remote: Error: Illegal version bump from '1.7.999' to '1.7.1000'. Check remote: http://bioconductor.org/developers/how-to/version-numbering/ remote: for details To git.bioconductor.org:packages/M3C.git ! [remote rejected] master -> master (pre-receive hook declined) error: failed to push some refs to 'g...@git.bioconductor.org: packages/M3C.git' Chris On Thu, 5 Sep 2019 at 11:17, Martin Morgan wrote: > This seems like a bug in the version check code. > > The next number after '999' is '1000', but '9991' is larger than '999', > too, so I think both 1000 and 9991 are valid version bumps; '10' is less > than '999' so is not a valid version bump. > > Note that .99... has no special significance in the third position (your > package will be bumped to 1.8.0 in release / 1.9.0 in devel at the next > release regardless...) so one would usually only get to '999' if one were a > very 'commit'ed person... ;) > > Martin > > On 9/5/19, 2:02 AM, "Bioc-devel on behalf of Christopher John" < > bioc-devel-boun...@r-project.org on behalf of chris.r.joh...@gmail.com> > wrote: > > This is just the update in the normal way to github, see the below > code. > > Please note the change from '1.7.999' to '1.7.10' as requested by Lori > unfortunately gives the same error message as before. Previously I > tried > version 1.7.9991 which didn't work. > > Any ideas? What is the correct version number to change to? > > Thanks, > > Chris > > ### update commands > > christopher@RA-MAP:~/M3C$ git checkout master > M DESCRIPTION > Already on 'master' > Your branch is up-to-date with 'origin/master'. > christopher@RA-MAP:~/M3C$ git add . > christopher@RA-MAP:~/M3C$ git commit -m "v no change" > [master 600273a] v no change > 1 file changed, 1 insertion(+), 1 deletion(-) > christopher@RA-MAP:~/M3C$ git push origin master > Username for 'https://github.com': crj32 > Password for 'https://cr...@github.com': > Counting objects: 3, done. > Delta compression using up to 16 threads. > Compressing objects: 100% (3/3), done. > Writing objects: 100% (3/3), 290 bytes | 290.00 KiB/s, done. > Total 3 (delta 2), reused 0 (delta 0) > remote: Resolving deltas: 100% (2/2), completed with 2 local objects. > To https://github.com/crj32/M3C >942ea47..600273a master -> master > christopher@RA-MAP:~/M3C$ git push upstream master > Counting objects: 8, done. > Delta compression using up to 16 threads. > Compressing objects: 100% (8/8), done. > Writing objects: 100% (8/8), 1.24 KiB | 1.24 MiB/s, done. > Total 8 (delta 6), reused 0 (delta 0) > > ### error > > remote: Error: Illegal version bump from '1.7.999' to '1.7.10'. Check > remote: http://bioconductor.org/developers/how-to/version-numbering/ > remote: for details > To git.bioconductor.org:packages/M3C.git > ! [remote rejected] master -> master (pre-receive hook declined) > error: failed to push some refs to 'g...@git.bioconductor.org: > packages/M3C.git' > > On Wed, 4 Sep 2019 at 14:57, Turaga, Nitesh < > nitesh.tur...@roswellpark.org> > wrote: > > > I suspect this was a Bioconductor hook rejecting the "version" > number? Is > > that correct Chris? > > > > Please also reply with the exact error message. > > > > Best, > > > > Nitesh > > > > > On Sep 4, 2019, at 7:58 AM, Shepherd, Lori > > > wrote: > > > > > > Or perhaps just providing the git commands you tried and the ERROR > that > > was produced with the original 1.7.9991 would be a better place to > start > > so we can evaluate the ERROR. > > > > > > > > > Cheers, > > > > > > > > > Lori Shepherd > > > > > > Bioconductor Core Team > > > > > > Roswell Park Cancer Institute > > > > > > Department of Biostatistics & Bioinformatics > > > > > > Elm & Carlton Streets > > > > > > Buffalo, New York 14263 > > > > > > > > > From: Bioc-devel on behalf of > > Christopher John > > > Sent: Wednesday, September 4, 2019 5:48:54 AM > > > To: bioc-devel@r-
Re: [Bioc-devel] Version number error
This is just the update in the normal way to github, see the below code. Please note the change from '1.7.999' to '1.7.10' as requested by Lori unfortunately gives the same error message as before. Previously I tried version 1.7.9991 which didn't work. Any ideas? What is the correct version number to change to? Thanks, Chris ### update commands christopher@RA-MAP:~/M3C$ git checkout master M DESCRIPTION Already on 'master' Your branch is up-to-date with 'origin/master'. christopher@RA-MAP:~/M3C$ git add . christopher@RA-MAP:~/M3C$ git commit -m "v no change" [master 600273a] v no change 1 file changed, 1 insertion(+), 1 deletion(-) christopher@RA-MAP:~/M3C$ git push origin master Username for 'https://github.com': crj32 Password for 'https://cr...@github.com': Counting objects: 3, done. Delta compression using up to 16 threads. Compressing objects: 100% (3/3), done. Writing objects: 100% (3/3), 290 bytes | 290.00 KiB/s, done. Total 3 (delta 2), reused 0 (delta 0) remote: Resolving deltas: 100% (2/2), completed with 2 local objects. To https://github.com/crj32/M3C 942ea47..600273a master -> master christopher@RA-MAP:~/M3C$ git push upstream master Counting objects: 8, done. Delta compression using up to 16 threads. Compressing objects: 100% (8/8), done. Writing objects: 100% (8/8), 1.24 KiB | 1.24 MiB/s, done. Total 8 (delta 6), reused 0 (delta 0) ### error remote: Error: Illegal version bump from '1.7.999' to '1.7.10'. Check remote: http://bioconductor.org/developers/how-to/version-numbering/ remote: for details To git.bioconductor.org:packages/M3C.git ! [remote rejected] master -> master (pre-receive hook declined) error: failed to push some refs to 'g...@git.bioconductor.org: packages/M3C.git' On Wed, 4 Sep 2019 at 14:57, Turaga, Nitesh wrote: > I suspect this was a Bioconductor hook rejecting the "version" number? Is > that correct Chris? > > Please also reply with the exact error message. > > Best, > > Nitesh > > > On Sep 4, 2019, at 7:58 AM, Shepherd, Lori > wrote: > > > > Or perhaps just providing the git commands you tried and the ERROR that > was produced with the original 1.7.9991 would be a better place to start > so we can evaluate the ERROR. > > > > > > Cheers, > > > > > > Lori Shepherd > > > > Bioconductor Core Team > > > > Roswell Park Cancer Institute > > > > Department of Biostatistics & Bioinformatics > > > > Elm & Carlton Streets > > > > Buffalo, New York 14263 > > > > > > From: Bioc-devel on behalf of > Christopher John > > Sent: Wednesday, September 4, 2019 5:48:54 AM > > To: bioc-devel@r-project.org > > Subject: [Bioc-devel] Version number error > > > > Hi > > > > I tried to update M3C as follows, and I got an error. What is wrong with > > the new version number please? What should it be? > > > > Version: 1.7.999 --> Version: 1.7.9991 > > > > Thanks, > > > > Chris > > > >[[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Version number error
Hi I tried to update M3C as follows, and I got an error. What is wrong with the new version number please? What should it be? Version: 1.7.999 --> Version: 1.7.9991 Thanks, Chris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Fwd: Version number update problem
Hi I tried to update as follows, and I got an error. What is wrong with the new version number please? Version: 1.7.999 --> Version: 1.7.9991 Thanks, Chris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Warning in 'CHECK' report for Windows machine after release version bump
Hi I also have a warning after the upgrade, just for the development version (I have not changed). I am not sure why this happened as I can't find the ape in the namespace and previously had no warning before upgrade. Thanks. * checking whether package ‘M3C’ can be installed ... WARNING Found the following significant warnings: Warning: S3 method ‘ape::as.phylo.dendrogram’ was declared in NAMESPACE but not found See ‘/Users/biocbuild/bbs-3.9-bioc/meat/M3C.Rcheck/00install.out’ for details. On Thu, 1 Nov 2018 at 08:09, Jakob Willforss wrote: > Hi! Getting closer to release, exciting! > > Today I saw that the build for my package NormalyzerDE gave a warning > after the release version bumps, > but only on the Windows build machine. No code has been changed from > previously succeeding builds. > > It seems to be unable to find certain functions in the libraries xts and > ggplot2 (see warning below). It seems to build fine on the Ubuntu and Mac > machines. > > Do you think this is something to worry about, or is it likely to be > something temporary to the build machines? I wonder in particular as my > work environment (and debugging environment of choice) is Linux, where the > problem don't seem to be reproduced. > > Best wishes, > Jakob > > The warning: > > * checking whether package ‘NormalyzerDE’ can be installed ... WARNING > Found the following significant warnings: > Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE > but not found > Warning: S3 methods ‘ggplot2::autoplot.zoo’, ‘ggplot2::fortify.zoo’ were > declared in NAMESPACE but not found > See ‘/Users/biocbuild/bbs-3.9-bioc/meat/NormalyzerDE.Rcheck/00install.out’ > for details. > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Changing the title of a package
Dear Bioconductor I want to change the title of my package, not the name. Is this OK to do as the next version bump just by changing the description field? Best wishes, Chris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Strange error for windows build
Dear Bioconductor I am getting a new weird error from today I think with my M3C package: http://bioconductor.org/packages/3.7/bioc/html/M3C.html Error in namespaceExport(ns, exports) : undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines ERROR: lazy loading failed for package 'M3C' * removing 'C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhoCTD/Rinst25246eb66cd0/M3C' In R CMD INSTALL --- ERROR: package installation failed Can anyone help me debug this? Thanks, Chris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Updating bioconductor after computer transfer - problem
Hi I have recently copy and pasted my github directory from my old PC to a new PC. I can update the github still fine, but bioconductor I get an error: christopher@RA-MAP:~/M3C$ git remote -v originhttps://github.com/crj32/M3C (fetch) originhttps://github.com/crj32/M3C (push) upstreamg...@git.bioconductor.org:packages/M3C.git (fetch) upstreamg...@git.bioconductor.org:packages/M3C.git (push) .. the usual commands christopher@RA-MAP:~/M3C$ git push origin master Username for 'https://github.com': crj32 Password for 'https://cr...@github.com': Everything up-to-date christopher@RA-MAP:~/M3C$ git push upstream master Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. I guessed this was to do with the ssh key not being update to date with the one from the new PC. So I followed the directions on this site and got my local ssh key, added it to the github, then sent the ssh key off to the bioconductor through the google forms page. Still no luck, same error. Was this the correct thing to do? https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Thanks, Chris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Version update question and an error?
Hi I have had a package quite recently accepted to the bioconductor. I have two questions: 1. My version is listed as 0.99.98 in my local description file, 1.1.0 in my bioconductor development web page, and 1.0.0 in the non development bioconductor web page. Do I bump to 1.1.1 in my next commit to the github? 2. I may have missed another email about this, but I noticed my development page has an error for build check for windows, but many other packages have this for windows atm, I checked the whole list. Is this something I need to worry about? Below is the error code: * checking for file 'M3C/DESCRIPTION' ... OK * preparing 'M3C': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR Many thanks, Chris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Vignette figures are wrong size
Dear Bioconductor
I checked my vignette using the knit option to biocstyle on my PC and the
figure sizes were all fine after some tweaking. However, in the online
vignette they have come out crazy small sizes. Previously I was resizing
them so they matched each other using the width command as shown below.
{width=40%}
Two days ago I dropped the width command incase it was causing problems
from all of the figures and the package has updated, but I am still having
the same problem with the copy on the bioconductor. On my local copy they
are all really big now because I dropped the resize parameter. Can you
help? I have the link to the package vignette below.
Kind Regards,
Chris
https://bioconductor.org/packages/devel/bioc/vignettes/M3C/inst/doc/M3Cvignette.html
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[Bioc-devel] Error following post acceptance instructions: permission denied
Hi I have had my package accepted to the bioconductor (M3C). I then followed the instructions in the email to add a ssh key to my account, then summited this to the bioconductor. I tested the key using the github instructions and it seemed to work fine. Next I ran: git remote add upstream g...@git.bioconductor.org:packages/M3C.git In my local M3C directory. The instructions are then to pull any upstream changes, the first command seems to work, but the second gives an error, why is this?: git fetch upstream Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. I am a bit confused at this point. Am I supposed to wait after submitting the key for a certain amount of time or have I done something wrong? Thanks, Chris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
