macs3-project/macsr

MACS3 R/BioC wrapper

macsr's Issues

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Error when installing MACSr

Hello,
I was trying to install MACSr under R4.1.0, Win10. However, it failed with the following error. I am not experienced with R, and wonder if you can give me some advice? I have Rtools installed. Thank you very much!

• installing source package 'MACSr' ...
  ** using non-staged installation via StagedInstall field
  ./configure.win: line 3: D:/Program: No such file or directory
  Warning in system("sh ./configure.win") : exit code 127
  ERROR: configuration failed for package 'MACSr'
• removing 'D:/Program Files/R/R-4.1.0/library/MACSr'

The downloaded source packages are in
‘C:\Users\zhuyi\AppData\Local\Temp\Rtmp65W18b\downloaded_packages’
Warning message:
In .inet_warning(msg) :
installation of package ‘MACSr’ had non-zero exit status

Error when calling callpeak function

Hi,

I tried calling callpeak on a BAM file:

callpeak("demux_testfastq_S1_L001_R1_001_aligned.bam")
Error in system2(python.cmd, c("-E", "-c", shQuote("print(1)")), stdout = TRUE, :
'"C:\Users\phily\AppData\Local\basilisk\1.3.6/0/python.exe"' not found

I'm using the R development version (4.1.0) and on Windows 10.

`callpeak`: `Error in py_module_import(module, convert = convert) : `

I've encountered an error when running callpeak, both with my custom files and the example code included in the documentation:

Reprex

Code

eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
CTRL <- eh[["EH4563"]]
res <- callpeak(CHIP, CTRL, gsize = 5.2e7,
                cutoff_analysis = TRUE,
                outdir = tempdir(),
                name = "callpeak_narrow0")

Console output

+ '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/0/bin/conda' 'create' '--yes' '--prefix' '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs' 'python=3.8.13' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs

  added / updated specs:
    - python=3.8.13


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bzip2-1.0.8                |       h0d85af4_4         155 KB  conda-forge
    ca-certificates-2022.9.24  |       h033912b_0         150 KB  conda-forge
    libffi-3.4.2               |       h0d85af4_5          50 KB  conda-forge
    libsqlite-3.39.3           |       ha978bb4_0         871 KB  conda-forge
    libzlib-1.2.12             |       hfd90126_3          65 KB  conda-forge
    ncurses-6.3                |       h96cf925_1         915 KB  conda-forge
    openssl-3.0.5              |       hfd90126_2         2.5 MB  conda-forge
    pip-22.2.2                 |     pyhd8ed1ab_0         1.5 MB  conda-forge
    python-3.8.13              |h66c20e1_0_cpython        12.8 MB  conda-forge
    readline-8.1.2             |       h3899abd_0         266 KB  conda-forge
    setuptools-65.4.0          |     pyhd8ed1ab_0         731 KB  conda-forge
    sqlite-3.39.3              |       h9ae0607_0         875 KB  conda-forge
    tk-8.6.12                  |       h5dbffcc_0         3.4 MB  conda-forge
    wheel-0.37.1               |     pyhd8ed1ab_0          31 KB  conda-forge
    xz-5.2.6                   |       h775f41a_0         233 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        24.4 MB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
  ca-certificates    conda-forge/osx-64::ca-certificates-2022.9.24-h033912b_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.39.3-ha978bb4_0
  libzlib            conda-forge/osx-64::libzlib-1.2.12-hfd90126_3
  ncurses            conda-forge/osx-64::ncurses-6.3-h96cf925_1
  openssl            conda-forge/osx-64::openssl-3.0.5-hfd90126_2
  pip                conda-forge/noarch::pip-22.2.2-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.8.13-h66c20e1_0_cpython
  readline           conda-forge/osx-64::readline-8.1.2-h3899abd_0
  setuptools         conda-forge/noarch::setuptools-65.4.0-pyhd8ed1ab_0
  sqlite             conda-forge/osx-64::sqlite-3.39.3-h9ae0607_0
  tk                 conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/0/bin/conda' 'install' '--yes' '--prefix' '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs' 'python=3.8.13'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.



==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 22.9.0

Please update conda by running

    $ conda update -n base -c defaults conda


+ '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/0/bin/conda' 'install' '--yes' '--prefix' '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs' '-c' 'conda-forge' 'python=3.8.13' 'numpy=1.17'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs

  added / updated specs:
    - numpy=1.17
    - python=3.8.13


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libblas-3.9.0              |16_osx64_openblas          13 KB  conda-forge
    libcblas-3.9.0             |16_osx64_openblas          13 KB  conda-forge
    libgfortran-5.0.0          |10_4_0_h97931a8_25         146 KB  conda-forge
    libgfortran5-11.3.0        |      h082f757_25         1.9 MB  conda-forge
    liblapack-3.9.0            |16_osx64_openblas          13 KB  conda-forge
    libopenblas-0.3.21         |openmp_h429af6e_3         9.6 MB  conda-forge
    llvm-openmp-14.0.4         |       ha654fa7_0         329 KB  conda-forge
    numpy-1.17.5               |   py38h6ced74f_1         5.0 MB  conda-forge
    python_abi-3.8             |           2_cp38           4 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        17.0 MB

The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-10_4_0_h97931a8_25
  libgfortran5       conda-forge/osx-64::libgfortran5-11.3.0-h082f757_25
  liblapack          conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3
  llvm-openmp        conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7_0
  numpy              conda-forge/osx-64::numpy-1.17.5-py38h6ced74f_1
  python_abi         conda-forge/osx-64::python_abi-3.8-2_cp38



Downloading and Extracting Packages
libgfortran5-11.3.0  | 1.9 MB    | ########## | 100% 
libgfortran-5.0.0    | 146 KB    | ########## | 100% 
libopenblas-0.3.21   | 9.6 MB    | ########## | 100% 
libblas-3.9.0        | 13 KB     | ########## | 100% 
numpy-1.17.5         | 5.0 MB    | ########## | 100% 
llvm-openmp-14.0.4   | 329 KB    | ########## | 100% 
python_abi-3.8       | 4 KB      | ########## | 100% 
liblapack-3.9.0      | 13 KB     | ########## | 100% 
libcblas-3.9.0       | 13 KB     | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 22.9.0

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting macs3==3.0.0a6
  Using cached MACS3-3.0.0a6.tar.gz (606 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting cykhash>=1.0.2
  Using cached cykhash-2.0.0-cp38-cp38-macosx_10_9_x86_64.whl
Requirement already satisfied: numpy>=1.17 in /Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs/lib/python3.8/site-packages (from macs3==3.0.0a6) (1.17.5)
Collecting Cython>=0.29
  Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB)
Building wheels for collected packages: macs3
  Building wheel for macs3 (pyproject.toml): started
  Building wheel for macs3 (pyproject.toml): still running...
  Building wheel for macs3 (pyproject.toml): finished with status 'done'
  Created wheel for macs3: filename=MACS3-3.0.0a6-cp38-cp38-macosx_10_9_x86_64.whl size=1853285 sha256=aadfab20998542cff254344b0efef4878c8aa63ea308f711570f8c3fec3659ae
  Stored in directory: /Users/schilder/Library/Caches/pip/wheels/95/4f/28/2ee87a153a82277a0adb1a1ab81ea9c97161e1f4eb1d9a0059
Successfully built macs3
Installing collected packages: cykhash, Cython, macs3
Successfully installed Cython-0.29.32 cykhash-2.0.0 macs3-3.0.0a6

Error

Error in py_module_import(module, convert = convert) : 
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 80 from PyObject

Session info

``` R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] MACSr_0.99.15 MACSdata_1.5.0 dplyr_1.0.10 TIPseeker_0.99.0

loaded via a namespace (and not attached):
[1] ica_1.0-3 RcppRoll_0.3.0
[3] class_7.3-20 Rsamtools_2.13.4
[5] lmtest_0.9-40 rprojroot_2.0.3
[7] crayon_1.5.1 spatstat.core_2.4-4
[9] MASS_7.3-58.1 nlme_3.1-159
[11] impute_1.71.0 basilisk_1.9.11
[13] GOSemSim_2.23.0 rlang_1.0.6
[15] XVector_0.37.1 ROCR_1.0-11
[17] readxl_1.4.1 irlba_2.3.5
[19] filelock_1.0.2 BiocParallel_1.31.12
[21] rjson_0.2.21 bit64_4.0.5
[23] glue_1.6.2 scKirby_0.1.0
[25] sctransform_0.3.5 parallel_4.2.1
[27] spatstat.sparse_2.1-1 AnnotationDbi_1.59.1
[29] BiocGenerics_0.43.4 DOSE_3.23.2
[31] spatstat.geom_2.4-0 tidyselect_1.1.2
[33] SummarizedExperiment_1.27.3 SeuratObject_4.1.2
[35] fitdistrplus_1.1-8 XML_3.99-0.10
[37] tidyr_1.2.1 zoo_1.8-11
[39] GenomicAlignments_1.33.1 xtable_1.8-4
[41] magrittr_2.0.3 evaluate_0.16
[43] ggplot2_3.3.6 cli_3.4.1
[45] zlibbioc_1.43.0 rstudioapi_0.14
[47] miniUI_0.1.1.1 sp_1.5-0
[49] rpart_4.1.16 fastmatch_1.1-3
[51] treeio_1.21.2 seqPattern_1.29.0
[53] EpiCompare_1.1.1 shiny_1.7.2
[55] xfun_0.33 ArchR_1.0.2
[57] cluster_2.1.4 genomation_1.29.0
[59] caTools_1.18.2 tidygraph_1.2.2
[61] KEGGREST_1.37.3 tibble_3.1.8
[63] interactiveDisplayBase_1.35.0 expm_0.999-6
[65] ggrepel_0.9.1 ape_5.6-2
[67] listenv_0.8.0 xlsxjars_0.6.1
[69] Biostrings_2.65.6 png_0.1-7
[71] future_1.28.0 withr_2.5.0
[73] bitops_1.0-7 ggforce_0.3.4
[75] aws.signature_0.6.0 plyr_1.8.7
[77] cellranger_1.1.0 e1071_1.7-11
[79] pillar_1.8.1 gplots_3.1.3
[81] cachem_1.0.6 GenomicFeatures_1.49.7
[83] vctrs_0.4.1 ellipsis_0.3.2
[85] generics_0.1.3 tools_4.2.1
[87] munsell_0.5.0 tweenr_2.0.2
[89] fgsea_1.23.2 aws.s3_0.3.21
[91] proxy_0.4-27 DelayedArray_0.23.2
[93] fastmap_1.1.0 compiler_4.2.1
[95] pkgload_1.3.0 abind_1.4-5
[97] httpuv_1.6.6 rtracklayer_1.57.0
[99] ExperimentHub_2.5.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[101] DescTools_0.99.46 plotly_4.10.0
[103] rgeos_0.5-9 rJava_1.0-6
[105] GenomeInfoDbData_1.2.8 gridExtra_2.3
[107] lattice_0.20-45 dir.expiry_1.5.1
[109] deldir_1.0-6 utf8_1.2.2
[111] later_1.3.0 BiocFileCache_2.5.0
[113] jsonlite_1.8.0 scales_1.2.1
[115] gld_2.6.5 tidytree_0.4.1
[117] pbapply_1.5-0 genefilter_1.79.0
[119] lazyeval_0.2.2 promises_1.2.0.1
[121] goftest_1.2-3 spatstat.utils_2.3-1
[123] reticulate_1.26 rmarkdown_2.16
[125] cowplot_1.1.1 Rtsne_0.16
[127] BSgenome_1.65.2 Biobase_2.57.1
[129] uwot_0.1.14 igraph_1.3.5
[131] survival_3.4-0 yaml_2.3.5
[133] plotrix_3.8-2 htmltools_0.5.3
[135] memoise_2.0.1 BiocIO_1.7.1
[137] Seurat_4.2.0 locfit_1.5-9.6
[139] graphlayouts_0.8.1 IRanges_2.31.2
[141] here_1.0.1 viridisLite_0.4.1
[143] digest_0.6.29 assertthat_0.2.1
[145] mime_0.12 rappdirs_0.3.3
[147] RSQLite_2.2.17 xlsx_0.6.5
[149] yulab.utils_0.0.5 future.apply_1.9.1
[151] Exact_3.2 data.table_1.14.2
[153] blob_1.2.3 S4Vectors_0.35.4
[155] splines_4.2.1 AnnotationHub_3.5.1
[157] RCurl_1.98-1.8 hms_1.1.2
[159] colorspace_2.0-3 BRGenomics_1.9.0
[161] base64enc_0.1-3 BiocManager_1.30.18
[163] GenomicRanges_1.49.1 aplot_0.1.7
[165] Signac_1.8.0 Rcpp_1.0.9
[167] RANN_2.6.1 mvtnorm_1.1-3
[169] enrichplot_1.17.2 fansi_1.0.3
[171] tzdb_0.3.0 parallelly_1.32.1
[173] ChIPseeker_1.33.2 R6_2.5.1
[175] grid_4.2.1 ggridges_0.5.4
[177] lifecycle_1.0.2 rootSolve_1.8.2.3
[179] curl_4.3.2 leiden_0.4.3
[181] DO.db_2.9 Matrix_1.5-1
[183] qvalue_2.29.0 RcppAnnoy_0.0.19
[185] RColorBrewer_1.1-3 stringr_1.4.1
[187] htmlwidgets_1.5.4 polyclip_1.10-0
[189] biomaRt_2.53.2 purrr_0.3.4
[191] shadowtext_0.1.2 gridGraphics_0.5-1
[193] mgcv_1.8-40 globals_0.16.1
[195] lmom_2.9 patchwork_1.1.2
[197] spatstat.random_2.2-0 progressr_0.11.0
[199] codetools_0.2-18 matrixStats_0.62.0
[201] GO.db_3.15.0 gtools_3.9.3
[203] prettyunits_1.1.1 dbplyr_2.2.1
[205] basilisk.utils_1.9.4 gridBase_0.4-7
[207] GenomeInfoDb_1.33.7 gtable_0.3.1
[209] DBI_1.1.3 stats4_4.2.1
[211] ggfun_0.0.7 tensor_1.5
[213] httr_1.4.4 KernSmooth_2.23-20
[215] stringi_1.7.8 progress_1.2.2
[217] reshape2_1.4.4 farver_2.1.1
[219] annotate_1.75.0 viridis_0.6.2
[221] ggtree_3.5.3 xml2_1.3.3
[223] boot_1.3-28 restfulr_0.0.15
[225] readr_2.1.2 geneplotter_1.75.0
[227] ggplotify_0.1.0 scattermore_0.8
[229] BiocVersion_3.16.0 DESeq2_1.37.6
[231] bit_4.0.4 scatterpie_0.1.8
[233] MatrixGenerics_1.9.1 spatstat.data_2.2-0
[235] ggraph_2.0.6 pkgconfig_2.0.3
[237] knitr_1.40

</details>