Install fails with BH 1.78.0-0 #49
Comments
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I am having the same issue with installing cytolib in the bioconductor/bioconductor_docker. |
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the bundled boost source code is out of sync, I will push the fix shortly |
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turned out the process of bundling the latest boost file system library is not straightforward as used to be, here is how I did it: extraction file system module from boost: Use foo/* to replace the existing old version of bundled file system library in cytolib, i.e.cytolib/src/boost/libs I will give it another try tomorrow |
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Hey @mikejiang. I know you've been investigating this, but I was looking at it as well and tracing the Anyway, you probably were already figuring all of that out and are working on a less hacky way to fix it, but just in case it helps at all I thought I'd mention it. |
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Thanks @jacobpwagner for pointing to the right direction, I ended up doing this |
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I have pushed the patch to bioconductor the latest release and development branch |
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Ah yes. Of course. Much better way. Thanks! |
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Installing into rocker/rstudio still crashes. |
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Any updates on the solutions? |
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If you are on the latest version of R and all the other packages, it should build |
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@mikejiang with the latest version of BH (1.81.0-1) it appears I have issues to compile the latest version of Cytolib (on Amazon Linux 2), could it be that the bundled boost code is out of sync again? |
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@FMKerckhof Thank you for reporting, patch is pushed |
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I have the same error. |
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@fbenedett : with the latest BH (CRAN) and cytolib (bioconductor) I was able to build on Ubuntu 22.04, 20.04, 18.04 and amazon linux 2 latest without any problems. Try to make sure you have the latest R, bioconductor (3.16) and it should work. My session on 22.04: |
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Dear All, Here is the last command for the g++ and the following errors and messages: We really need to get it up and running soon. I do not want to buy the flowjo 😢 |
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More details in case they are needed: Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 20.1
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.0
[5] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.1.8
[9] ggplot2_3.4.1 tidyverse_2.0.0 BH_1.81.0-1 BiocManager_1.30.20
loaded via a namespace (and not attached):
[1] compiler_4.2.2 pillar_1.8.1 tools_4.2.2 digest_0.6.31 timechange_0.2.0
[6] evaluate_0.20 lifecycle_1.0.3 gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6
[11] cli_3.6.0 rstudioapi_0.14 yaml_2.3.7 xfun_0.37 fastmap_1.1.1
[16] withr_2.5.0 knitr_1.42 generics_0.1.3 vctrs_0.5.2 hms_1.1.2
[21] grid_4.2.2 tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4
[26] rmarkdown_2.20 tzdb_0.3.0 magrittr_2.0.3 scales_1.2.1 htmltools_0.5.4
[31] ellipsis_0.3.2 colorspace_2.1-0 utf8_1.2.3 stringi_1.7.12 munsell_0.5.0 ``` |
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Hi @LuisaFJimenez I don't know enough about the C++ internals of cytolib, but are you sure you have latest BioConductor? I had to update to 3.16 for things to work |
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Hi @FMKerckhof ... I checked again... that was the trick. For some reason I had in my mind that if I had the latest BiocManager updated, that was equivalent to having the latest Bioconductor... it was not. As soon as I added the command you wrote, it installed 40 new updates/packages. The flowCore and the cytolib are running smoothly. Thanks a lot! |
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Hello, I'm also having issues installing, I'm running latest version of R (4.2.3) and Bioconductor (3.16). My session info is below. Any suggestions would be much appreciated. |
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It seems there may be a new mismatch with the recent release of BH 1.87.0-1 from CRAN (eddelbuettel/bh@f920423) - @mikejiang quick ping just to assess if you are aware of the issue. I include below some logs from a packrat restore on ubuntu 22.04, R 4.4.2: |
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bioconductor the latest develop and release branches seem to build fine |
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It looks like bioconductor just updated their build system now and the same error is reproduced from their latest report. I will patch it up |
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updated de79a5d |
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Describe the bug
Install proceeds fully with BH 1.75.0-0 (installed from source), but with 1.78.0-0 I get the following error traceback. Appears to be an issue with
boost/libs/filesystem/src/path.o?SessionInfo:
The text was updated successfully, but these errors were encountered: