Closed wenbostar closed 5 years ago
Session info?
For haematopoiesis dataset, I just tried again and the error was gone. But for pancreas dataset, I got the following error:
adding rname 'https://jmlab-gitlab.cruk.cam.ac.uk/publications/MNN2017-DataFiles/raw/4d649e8865cb2b924b61f6bd3f908865dfe0f560/GSE86473//GSE86473_experimental_design.tsv'
|======================================================================| 100%
Error in bfcrpath(bfc, file.path(host.path, "GSE86473_experimental_design.tsv")) :
not all 'rnames' found or unique.
1: In isOutlier(sce.gse81076$scater_qc$feature_control_ERCC$pct_counts, :
missing values ignored during outlier detection
2: download failed
web resource path: ‘https://jmlab-gitlab.cruk.cam.ac.uk/publications/MNN2017-DataFiles/raw/4d649e8865cb2b924b61f6bd3f908865dfe0f560/GSE86473//GSE86473_experimental_design.tsv’
local file path: ‘/Users/wb/Library/Caches/BiocFileCache/b53561eff5e_GSE86473_experimental_design.tsv’
reason: Not Found (HTTP 404).
3: bfcadd() failed; resource removed
rid: BFC20
fpath: ‘https://jmlab-gitlab.cruk.cam.ac.uk/publications/MNN2017-DataFiles/raw/4d649e8865cb2b924b61f6bd3f908865dfe0f560/GSE86473//GSE86473_experimental_design.tsv’
reason: download failed
4: In value[[3L]](cond) :
trying to add rname 'https://jmlab-gitlab.cruk.cam.ac.uk/publications/MNN2017-DataFiles/raw/4d649e8865cb2b924b61f6bd3f908865dfe0f560/GSE86473//GSE86473_experimental_design.tsv' produced error:
bfcadd() failed; see warnings()
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.3
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocFileCache_1.6.0 dbplyr_1.3.0
[3] scater_1.10.1 ggplot2_3.1.0
[5] biomaRt_2.38.0 scran_1.10.2
[7] SingleCellExperiment_1.4.1 SummarizedExperiment_1.12.0
[9] DelayedArray_0.8.0 matrixStats_0.54.0
[11] Biobase_2.42.0 GenomicRanges_1.34.0
[13] GenomeInfoDb_1.18.2 IRanges_2.16.0
[15] S4Vectors_0.20.1 BiocGenerics_0.28.0
[17] BiocParallel_1.16.6
loaded via a namespace (and not attached):
[1] viridis_0.5.1 httr_1.4.0 dynamicTreeCut_1.63-1
[4] edgeR_3.24.3 bit64_0.9-7 viridisLite_0.3.0
[7] DelayedMatrixStats_1.4.0 assertthat_0.2.0 statmod_1.4.30
[10] blob_1.1.1 GenomeInfoDbData_1.2.0 vipor_0.4.5
[13] progress_1.2.0 pillar_1.3.1 RSQLite_2.1.1
[16] lattice_0.20-38 glue_1.3.0 limma_3.38.3
[19] digest_0.6.18 XVector_0.22.0 colorspace_1.4-0
[22] Matrix_1.2-15 plyr_1.8.4 XML_3.98-1.17
[25] pkgconfig_2.0.2 zlibbioc_1.28.0 purrr_0.3.0
[28] scales_1.0.0 HDF5Array_1.10.1 tibble_2.0.1
[31] withr_2.1.2 lazyeval_0.2.1 magrittr_1.5
[34] crayon_1.3.4 memoise_1.1.0 beeswarm_0.2.3
[37] tools_3.5.1 prettyunits_1.0.2 hms_0.4.2
[40] stringr_1.4.0 Rhdf5lib_1.4.2 munsell_0.5.0
[43] locfit_1.5-9.1 irlba_2.3.3 AnnotationDbi_1.44.0
[46] compiler_3.5.1 rlang_0.3.1 rhdf5_2.26.2
[49] grid_3.5.1 RCurl_1.95-4.11 BiocNeighbors_1.0.0
[52] rappdirs_0.3.1 igraph_1.2.4 bitops_1.0-6
[55] gtable_0.2.0 curl_3.3 DBI_1.0.0
[58] reshape2_1.4.3 R6_2.4.0 gridExtra_2.3
[61] dplyr_0.8.0.1 bit_1.1-14 stringi_1.3.1
[64] ggbeeswarm_0.6.0 Rcpp_1.0.0 tidyselect_0.2.5
Yes, that will be fixed later today. I was going to update these scripts anyway, so you're in luck.
It's great. Thanks.
Should be fixed by 4f00208544d8c07730134a98a05a3288ade0869d. Be aware that the corresponding correction script hasn't been updated, so YMMV until I get around to it tomorrow.
I got the following error for your new version:
setwd("FurtherMNN2018/haematopoiesis")
library(rmarkdown)
render("prepare.Rmd")
label: unnamed-chunk-8
|............................ | 42%
ordinary text without R code
|.............................. | 45%
label: unnamed-chunk-9
Attaching package: 'BiocSingular'
The following object is masked from 'package:scater':
runPCA
Quitting from lines 94-98 (prepare.Rmd)
Error in cutreeDynamic(htree, minClusterSize = min.size, distM = as.matrix(distM), :
unused arguments (use.ranks = FALSE, BSPARAM = IrlbaParam())
Calls: render ... quickCluster -> quickCluster -> .local -> .quick_cluster -> unname
If you're running a Bioc-devel build, then scran was just updated last night - 1.1.20.
Still got error after I updated scran to 1.11.20:
library(rmarkdown)
render("prepare.Rmd")
|........................... | 40%
label: unnamed-chunk-8
|............................ | 42%
ordinary text without R code
|.............................. | 45%
label: unnamed-chunk-9
Attaching package: 'BiocSingular'
The following object is masked from 'package:scater':
runPCA
Quitting from lines 94-98 (prepare.Rmd)
Error in .local(x, ...) : unused argument (BSPARAM = IrlbaParam())
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Amazon Linux AMI 2018.03
Matrix products: default
BLAS: /home/test/software/R/3/lib64/R/lib/libRblas.so
LAPACK: /home/test/software/R/3/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocSingular_0.99.12 scran_1.11.20
[3] scater_1.10.1 ggplot2_3.1.0
[5] SingleCellExperiment_1.4.1 SummarizedExperiment_1.12.0
[7] DelayedArray_0.8.0 BiocParallel_1.16.6
[9] matrixStats_0.54.0 Biobase_2.42.0
[11] GenomicRanges_1.34.0 GenomeInfoDb_1.18.2
[13] IRanges_2.16.0 S4Vectors_0.20.1
[15] BiocGenerics_0.28.0 BiocFileCache_1.6.0
[17] dbplyr_1.3.0 BiocStyle_2.10.0
[19] rmarkdown_1.11
loaded via a namespace (and not attached):
[1] dynamicTreeCut_1.63-1 viridis_0.5.1 httr_1.4.0
[4] edgeR_3.24.3 bit64_0.9-7 viridisLite_0.3.0
[7] DelayedMatrixStats_1.4.0 assertthat_0.2.0 statmod_1.4.30
[10] BiocManager_1.30.4 blob_1.1.1 GenomeInfoDbData_1.2.0
[13] vipor_0.4.5 yaml_2.2.0 pillar_1.3.1
[16] RSQLite_2.1.1 lattice_0.20-38 limma_3.38.3
[19] glue_1.3.0 digest_0.6.18 XVector_0.22.0
[22] colorspace_1.4-0 htmltools_0.3.6 Matrix_1.2-15
[25] plyr_1.8.4 pkgconfig_2.0.2 bookdown_0.9
[28] zlibbioc_1.28.0 purrr_0.3.1 scales_1.0.0
[31] HDF5Array_1.10.1 tibble_2.0.1 withr_2.1.2
[34] lazyeval_0.2.1 magrittr_1.5 crayon_1.3.4
[37] memoise_1.1.0 evaluate_0.13 beeswarm_0.2.3
[40] tools_3.5.1 stringr_1.4.0 Rhdf5lib_1.4.2
[43] locfit_1.5-9.1 munsell_0.5.0 irlba_2.3.3
[46] compiler_3.5.1 rsvd_1.0.0 rlang_0.3.1
[49] rhdf5_2.26.2 grid_3.5.1 RCurl_1.95-4.12
[52] BiocNeighbors_1.1.12 rappdirs_0.3.1 igraph_1.2.4
[55] bitops_1.0-6 gtable_0.2.0 DBI_1.0.0
[58] curl_3.3 reshape2_1.4.3 R6_2.4.0
[61] gridExtra_2.3 knitr_1.21 dplyr_0.8.0.1
[64] bit_1.1-14 stringi_1.3.1 ggbeeswarm_0.6.0
[67] Rcpp_1.0.0 tidyselect_0.2.5 xfun_0.5
>
You're using a crazy mix of Bioc-devel and Bioc-release packages. Get BiocManager::valid()
and try it again. This will require R-devel - a bit annoying, but all of these packages are under active development.
When I tried to install the version of scran in Bioc release channel, I got the following error. This is why I installed the version in Bioc devel channel.
BiocManager::install("scran")
** R
** inst
** byte-compile and prepare package for lazy loading
Error : object ‘buildNNIndex’ is not exported by 'namespace:BiocNeighbors'
ERROR: lazy loading failed for package ‘scran’
* removing ‘/home/test/software/R/3/lib64/R/library/scran’
* restoring previous ‘/home/test/software/R/3/lib64/R/library/scran’
The downloaded source packages are in
‘/tmp/RtmpzHeWUJ/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ‘scran’ had non-zero exit status
All of these problems arise from the same underlying source; you are mixing release and devel pacake versions and thus your installation is not BiocManager::valid()
. The Bioc-devel version of scran requires the Bioc-devel version of BiocNeighbors and so on. This applies to other packages as well, e.g., S4Vectors, BiocParallel. You are making life difficult for yourself (and anyone trying to help you) by manually mixing release and devel versions together. So:
install.packages("BiocManager")
.BiocManager::install("scran")
.I'm using R 3.5.1. Does FurtherMNN2018 only work well under R-devel?
The FurtherMNN2018
code itself doesn't care what version of R you're on. But batchelor was written in mind for submission to Bioconductor 3.9, which uses R-devel (to be R 3.6 later this year).
I just followed your suggestion to have the R-devel installed. However, I got the same error as show below:
library(rmarkdown)
render("prepare.Rmd")
label: unnamed-chunk-8
|............................ | 42%
ordinary text without R code
|.............................. | 45%
label: unnamed-chunk-9
Quitting from lines 94-98 (prepare.Rmd)
Error in .local(x, ...) : unused argument (BSPARAM = IrlbaParam())
> sessionInfo()
R Under development (unstable) (2019-03-03 r76192)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Amazon Linux AMI 2018.03
Matrix products: default
BLAS: /home/test/software/R/dev/lib64/R/lib/libRblas.so
LAPACK: /home/test/software/R/dev/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocSingular_0.99.12 scran_1.11.20
[3] scater_1.11.12 ggplot2_3.1.0
[5] SingleCellExperiment_1.5.2 SummarizedExperiment_1.13.0
[7] DelayedArray_0.9.8 BiocParallel_1.17.17
[9] matrixStats_0.54.0 Biobase_2.43.1
[11] GenomicRanges_1.35.1 GenomeInfoDb_1.19.2
[13] IRanges_2.17.4 S4Vectors_0.21.10
[15] BiocGenerics_0.29.1 BiocFileCache_1.7.0
[17] dbplyr_1.3.0 BiocStyle_2.11.0
[19] rmarkdown_1.11
loaded via a namespace (and not attached):
[1] viridis_0.5.1 httr_1.4.0 dynamicTreeCut_1.63-1
[4] edgeR_3.25.3 bit64_0.9-7 viridisLite_0.3.0
[7] DelayedMatrixStats_1.5.2 assertthat_0.2.0 statmod_1.4.30
[10] BiocManager_1.30.4 blob_1.1.1 GenomeInfoDbData_1.2.0
[13] vipor_0.4.5 yaml_2.2.0 pillar_1.3.1
[16] RSQLite_2.1.1 lattice_0.20-38 limma_3.39.12
[19] glue_1.3.0 digest_0.6.18 XVector_0.23.0
[22] colorspace_1.4-0 htmltools_0.3.6 Matrix_1.2-15
[25] plyr_1.8.4 pkgconfig_2.0.2 bookdown_0.9
[28] zlibbioc_1.29.0 purrr_0.3.1 scales_1.0.0
[31] tibble_2.0.1 withr_2.1.2 lazyeval_0.2.1
[34] magrittr_1.5 crayon_1.3.4 memoise_1.1.0
[37] evaluate_0.13 beeswarm_0.2.3 tools_3.6.0
[40] stringr_1.4.0 locfit_1.5-9.1 munsell_0.5.0
[43] irlba_2.3.3 compiler_3.6.0 rsvd_1.0.0
[46] rlang_0.3.1 grid_3.6.0 RCurl_1.95-4.12
[49] BiocNeighbors_1.1.12 rappdirs_0.3.1 igraph_1.2.4
[52] bitops_1.0-6 gtable_0.2.0 DBI_1.0.0
[55] curl_3.3 R6_2.4.0 gridExtra_2.3
[58] knitr_1.21 dplyr_0.8.0.1 bit_1.1-14
[61] stringi_1.3.1 ggbeeswarm_0.6.0 Rcpp_1.0.0
[64] tidyselect_0.2.5 xfun_0.5
>
I don't know why this error is happening for you. Setting BSPARAM=
in quickCluster()
works for me, and it compiles elsewhere. Try it locally instead of on an AMI.
This parameter (BSPARAM = IrlbaParam()) is used by which function? I don't find this parameter in function quickCluster.
grep BSPARAM prepare.Rmd
clustF <- quickCluster(sceF, use.ranks=FALSE, BSPARAM=IrlbaParam())
The problem has been fixed after I installed the scran from https://github.com/MarioniLab/scran. Looks like the version of scran (1.11.20) from Bioc-devel branch doesn't have parameter "BSPARAM".
Hm... looks like Bioconductor's source package is somehow out of date with the reference manual on the same page. I bumped the version a few days ago, so this will get fixed with 1.11.21; in the meantime, just use the GitHub version.
I got the following error when I tried to run "haematopoiesis/prepareData.R":
How can I fix this problem?