Error on "getpromoters" on hg38

I want to use on my chipseq this tools. I have alligned on hg38.


library("ChIPseeker")
library("TxDb.Hsapiens.UCSC.hg38.knownGene")
setwd("~/Desktop/RESULTS2rip/")
files=list.files("chr_hg38",full.names=T)
files
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
peakfile=readPeakFile(files[1])
promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000)

Error in `seqlevels<-`(`*tmp*`, force = TRUE, value = c("chr1", "chr2",  :
  unused argument (force = TRUE)

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /home/maurizio/miniconda2/envs/delete/lib/R/lib/libRblas.so
LAPACK: /home/maurizio/miniconda2/envs/delete/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 GenomicFeatures_1.26.4                 
 [3] AnnotationDbi_1.40.0                    Biobase_2.38.0                         
 [5] GenomicRanges_1.30.0                    GenomeInfoDb_1.14.0                    
 [7] IRanges_2.12.0                          S4Vectors_0.16.0                       
 [9] BiocGenerics_0.24.0                     ChIPseeker_1.14.0                      

loaded via a namespace (and not attached):
 [1] bit64_0.9-7                             splines_3.4.1                          
 [3] gtools_3.5.0                            assertthat_0.2.0                       
 [5] DO.db_2.9                               rvcheck_0.0.9                          
 [7] blob_1.1.0                              GenomeInfoDbData_1.0.0                 
 [9] Rsamtools_1.30.0                        pillar_1.1.0                           
[11] RSQLite_2.0                             lattice_0.20-35                        
[13] glue_1.2.0                              digest_0.6.15                          
[15] RColorBrewer_1.1-2                      XVector_0.18.0                         
[17] qvalue_2.10.0                           colorspace_1.3-2                       
[19] Matrix_1.2-12                           plyr_1.8.4                             
[21] XML_3.98-1.10                           pkgconfig_2.0.1                        
[23] biomaRt_2.32.1                          zlibbioc_1.24.0                        
[25] GO.db_3.5.0                             scales_0.5.0                           
[27] gdata_2.18.0                            BiocParallel_1.12.0                    
[29] tibble_1.4.2                            ggplot2_2.2.1                          
[31] UpSetR_1.3.3                            SummarizedExperiment_1.4.0             
[33] lazyeval_0.2.1                          magrittr_1.5                           
[35] memoise_1.1.0                           DOSE_3.4.0                             
[37] gplots_3.0.1                            tools_3.4.1                            
[39] data.table_1.10.4-3                     gridBase_0.4-7                         
[41] stringr_1.3.0                           munsell_0.4.3                          
[43] plotrix_3.6-6                           bindrcpp_0.2                           
[45] Biostrings_2.46.0                       compiler_3.4.1                         
[47] caTools_1.17.1                          rlang_0.2.0                            
[49] grid_3.4.1                              RCurl_1.95-4.10                        
[51] igraph_1.1.2                            bitops_1.0-6                           
[53] boot_1.3-20                             gtable_0.2.0                           
[55] DBI_0.7                                 reshape2_1.4.3                         
[57] R6_2.2.2                                GenomicAlignments_1.10.0               
[59] gridExtra_2.3                           dplyr_0.7.4                            
[61] rtracklayer_1.38.0                      bit_1.1-12                             
[63] bindr_0.1                               fastmatch_1.1-0                        
[65] fgsea_1.4.0                             KernSmooth_2.23-15                     
[67] GOSemSim_2.4.0                          stringi_1.1.6                          
[69] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 Rcpp_0.12.15

Can't reproduce your issue.

wx20180227-143600

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] ChIPseeker_1.15.3
 [2] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0
 [3] GenomicFeatures_1.30.3
 [4] AnnotationDbi_1.40.0
 [5] Biobase_2.38.0
 [6] GenomicRanges_1.30.3
 [7] GenomeInfoDb_1.14.0
 [8] IRanges_2.12.0
 [9] S4Vectors_0.16.0
[10] BiocGenerics_0.24.0
[11] rvcheck_0.0.9
[12] colorout_1.1-3
[13] rmarkdown_1.8
[14] roxygen2_6.0.1
[15] magrittr_1.5
[16] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] bitops_1.0-6
 [2] matrixStats_0.53.1
 [3] enrichplot_0.99.11
 [4] devtools_1.13.5
 [5] bit64_0.9-7
 [6] RColorBrewer_1.1-2
 [7] progress_1.1.2
 [8] httr_1.3.1
 [9] rprojroot_1.3-2
[10] UpSetR_1.3.3
[11] tools_3.4.3
[12] backports_1.1.2
[13] R6_2.2.2
[14] KernSmooth_2.23-15
[15] DBI_0.7
[16] lazyeval_0.2.1
[17] colorspace_1.3-2
[18] withr_2.1.1
[19] gridExtra_2.3
[20] prettyunits_1.0.2
[21] RMySQL_0.10.13
[22] bit_1.1-12
[23] compiler_3.4.3
[24] xml2_1.2.0
[25] DelayedArray_0.4.1
[26] rtracklayer_1.38.3
[27] caTools_1.17.1
[28] scales_0.5.0
[29] ggridges_0.4.1
[30] commonmark_1.4
[31] stringr_1.3.0
[32] digest_0.6.15
[33] Rsamtools_1.30.0
[34] DOSE_3.5.1
[35] XVector_0.18.0
[36] pkgconfig_2.0.1
[37] htmltools_0.3.6
[38] plotrix_3.7
[39] rlang_0.2.0
[40] rstudioapi_0.7
[41] RSQLite_2.0
[42] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[43] bindr_0.1
[44] gtools_3.5.0
[45] BiocParallel_1.12.0
[46] GOSemSim_2.5.1
[47] dplyr_0.7.4
[48] RCurl_1.95-4.10
[49] GO.db_3.5.0
[50] GenomeInfoDbData_1.0.0
[51] Matrix_1.2-12
[52] Rcpp_0.12.15
[53] munsell_0.4.3
[54] viridis_0.5.0
[55] stringi_1.1.6
[56] ggraph_1.0.1
[57] MASS_7.3-49
[58] SummarizedExperiment_1.8.1
[59] zlibbioc_1.24.0
[60] gplots_3.0.1
[61] plyr_1.8.4
[62] qvalue_2.10.0
[63] grid_3.4.3
[64] blob_1.1.0
[65] gdata_2.18.0
[66] ggrepel_0.7.0
[67] DO.db_2.9
[68] udunits2_0.13
[69] lattice_0.20-35
[70] Biostrings_2.46.0
[71] cowplot_0.9.2
[72] splines_3.4.3
[73] knitr_1.20
[74] pillar_1.2.0
[75] fgsea_1.4.1
[76] igraph_1.1.2
[77] boot_1.3-20
[78] reshape2_1.4.3
[79] biomaRt_2.34.2
[80] fastmatch_1.1-0
[81] XML_3.98-1.10
[82] glue_1.2.0
[83] evaluate_0.10.1
[84] data.table_1.10.4-3
[85] tweenr_0.1.5
[86] gtable_0.2.0
[87] assertthat_0.2.0
[88] ggplot2_2.2.1
[89] gridBase_0.4-7
[90] ggforce_0.1.1
[91] viridisLite_0.3.0
[92] tibble_1.4.2
[93] GenomicAlignments_1.14.1
[94] memoise_1.1.0
[95] units_0.5-1
[96] bindrcpp_0.2
>

I have this problem using conda with bioconda installation..

Il 27 febbraio 2018 alle 7.38 Guangchuang Yu notifications@github.com ha scritto:

Can't reproduce your issue.

[wx20180227-143600] https://user-images.githubusercontent.com/626539/36714091-a6eec3c6-1bcb-11e8-9ee4-166ebf48a513.png

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] ChIPseeker_1.15.3
 [2] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0
 [3] GenomicFeatures_1.30.3
 [4] AnnotationDbi_1.40.0
 [5] Biobase_2.38.0
 [6] GenomicRanges_1.30.3
 [7] GenomeInfoDb_1.14.0
 [8] IRanges_2.12.0
 [9] S4Vectors_0.16.0
[10] BiocGenerics_0.24.0
[11] rvcheck_0.0.9
[12] colorout_1.1-3
[13] rmarkdown_1.8
[14] roxygen2_6.0.1
[15] magrittr_1.5
[16] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] bitops_1.0-6
 [2] matrixStats_0.53.1
 [3] enrichplot_0.99.11
 [4] devtools_1.13.5
 [5] bit64_0.9-7
 [6] RColorBrewer_1.1-2
 [7] progress_1.1.2
 [8] httr_1.3.1
 [9] rprojroot_1.3-2
[10] UpSetR_1.3.3
[11] tools_3.4.3
[12] backports_1.1.2
[13] R6_2.2.2
[14] KernSmooth_2.23-15
[15] DBI_0.7
[16] lazyeval_0.2.1
[17] colorspace_1.3-2
[18] withr_2.1.1
[19] gridExtra_2.3
[20] prettyunits_1.0.2
[21] RMySQL_0.10.13
[22] bit_1.1-12
[23] compiler_3.4.3
[24] xml2_1.2.0
[25] DelayedArray_0.4.1
[26] rtracklayer_1.38.3
[27] caTools_1.17.1
[28] scales_0.5.0
[29] ggridges_0.4.1
[30] commonmark_1.4
[31] stringr_1.3.0
[32] digest_0.6.15
[33] Rsamtools_1.30.0
[34] DOSE_3.5.1
[35] XVector_0.18.0
[36] pkgconfig_2.0.1
[37] htmltools_0.3.6
[38] plotrix_3.7
[39] rlang_0.2.0
[40] rstudioapi_0.7
[41] RSQLite_2.0
[42] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[43] bindr_0.1
[44] gtools_3.5.0
[45] BiocParallel_1.12.0
[46] GOSemSim_2.5.1
[47] dplyr_0.7.4
[48] RCurl_1.95-4.10
[49] GO.db_3.5.0
[50] GenomeInfoDbData_1.0.0
[51] Matrix_1.2-12
[52] Rcpp_0.12.15
[53] munsell_0.4.3
[54] viridis_0.5.0
[55] stringi_1.1.6
[56] ggraph_1.0.1
[57] MASS_7.3-49
[58] SummarizedExperiment_1.8.1
[59] zlibbioc_1.24.0
[60] gplots_3.0.1
[61] plyr_1.8.4
[62] qvalue_2.10.0
[63] grid_3.4.3
[64] blob_1.1.0
[65] gdata_2.18.0
[66] ggrepel_0.7.0
[67] DO.db_2.9
[68] udunits2_0.13
[69] lattice_0.20-35
[70] Biostrings_2.46.0
[71] cowplot_0.9.2
[72] splines_3.4.3
[73] knitr_1.20
[74] pillar_1.2.0
[75] fgsea_1.4.1
[76] igraph_1.1.2
[77] boot_1.3-20
[78] reshape2_1.4.3
[79] biomaRt_2.34.2
[80] fastmatch_1.1-0
[81] XML_3.98-1.10
[82] glue_1.2.0
[83] evaluate_0.10.1
[84] data.table_1.10.4-3
[85] tweenr_0.1.5
[86] gtable_0.2.0
[87] assertthat_0.2.0
[88] ggplot2_2.2.1
[89] gridBase_0.4-7
[90] ggforce_0.1.1
[91] viridisLite_0.3.0
[92] tibble_1.4.2
[93] GenomicAlignments_1.14.1
[94] memoise_1.1.0
[95] units_0.5-1
[96] bindrcpp_0.2
>

—
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I have the same problem, and I am also using bioconda:

> promoter <- getPromoters(TxDb = txdb, upstream=3000,downstream=3000)
Error in `seqlevels<-`(`*tmp*`, force = TRUE, value = c("chr1", "chr2",  : 
  unused argument (force = TRUE)

I wonder if it has anything to do with the absence of the RMySQL package:

> library(ChIPseeker)

Warning: namespace 'RMySQL' is not available and has been replaced
by .GlobalEnv when processing object 'plot.index'
Warning: namespace 'RMySQL' is not available and has been replaced
by .GlobalEnv when processing object 'plot.index'

Which is a package that conda fails to install. If that's the case, I understand it is not an issue related with ChIPseeker, but with conda.

$ conda install -c bioconda r-rmysql
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
  - bioconductor-biocgenerics
  - defaults/linux-64::ruamel_yaml==0.15.35=py36h14c3975_1
  - defaults/linux-64::tk==8.6.7=hc745277_3
  - r-rmysql
Use "conda info <package>" to see the dependencies for each package.

It's me again, so after some more investigation I discovered that the issue is related to a dependency conflict in conda.

Basically, the bioconductor package that is producing the error is GenomicFeatures

The version that conda allows you to install is 2.16, which causes the error. If you forget about conda, and install all the packages with bioconductor, you get the version 1.30 that works fine.

You can find version 1.30 in the conda repository, but then it will install the icu package version > 54 that will fail later on when you run R.

conda create -p ~/test conda bioconductor-ChIPseeker bioconductor-genomicfeatures=1.30
[..]
> library(ChIPseeker)

Error: package or namespace load failed for 'ChIPseeker' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '~/test/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.54: cannot open shared object file: No such file or directory

And, if you try to force versions, then you have a unresolvable version conflict:

$ conda create -p ~/test conda bioconductor-ChIPseeker bioconductor-genomicfeatures=1.30 icu=54.1
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
  - bioconductor-genomicfeatures=1.30
  - icu=54.1
Use "conda info <package>" to see the dependencies for each package.

So it is a version dependency problem, I don't think there is anything to do here except perhaps enforce somehow that the version of GenomicFeatures has to be at least 1.30.

I have the same problem and the folloing steps works with me(using R 3.4.1): conda install bioconductor-clusterprofile conda install bioconductor-chipseeker start R and enter: remove.packages("GenomicFeatures") quit R conda install bioconductor-genomicfeatures

conda will automatically install bioconductor-genomicfeatures-1.30.3 and it will work!

YuLab-SMU / ChIPseeker

Error on "getpromoters" on hg38 #74