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Hello. Not sure if this is an issue. The website shows 331 lines of tools/packages after installation. My installation shows only 305. Would this be due to R version?
library(powsimR)
Loading required package: gamlss.dist
Loading required package: MASS
Warning messages:
1: replacing previous import ‘DECENT::lrTest’ by ‘MAST::lrTest’ when loading ‘powsimR’
2: replacing previous import ‘parallel::makeCluster’ by ‘snow::makeCluster’ when loading ‘powsimR’
3: replacing previous import ‘parallel::stopCluster’ by ‘snow::stopCluster’ when loading ‘powsimR’
4: replacing previous import ‘penalized::predict’ by ‘stats::predict’ when loading ‘powsimR’
5: replacing previous import ‘zinbwave::glmWeightedF’ by ‘zingeR::glmWeightedF’ when loading ‘powsimR’
sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.3 (Nitrogen)
so the lines of the sessionInfo() is not from a cleaned up installation on my system, ie. that also other packages that I have installed are printed. Since you have powsimR listed as attached you should be ready to go.
Hello. Not sure if this is an issue. The website shows 331 lines of tools/packages after installation. My installation shows only 305. Would this be due to R version?
Matrix products: default
BLAS: /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] powsimR_1.1.2 gamlss.dist_5.0-6 MASS_7.3-50
loaded via a namespace (and not attached):
[1] mixtools_1.1.0 softImpute_1.4
[3] minpack.lm_1.2-1 pbapply_1.3-4
[5] lattice_0.20-35 haven_1.1.2
[7] fastICA_1.2-1 mgcv_1.8-24
[9] penalized_0.9-51 blob_1.1.1
[11] survival_2.42-6 later_0.7.3
[13] nloptr_1.0.4 DBI_1.0.0
[15] R.utils_2.6.0 SingleCellExperiment_1.0.0
[17] Linnorm_2.2.0 bindr_0.1.1
[19] zlibbioc_1.24.0 MatrixModels_0.4-1
[21] pspline_1.0-18 pcaMethods_1.70.0
[23] SDMTools_1.1-221 htmlwidgets_1.2
[25] mvtnorm_1.0-8 hdf5r_1.0.0
[27] UpSetR_1.3.3 parallel_3.4.3
[29] scater_1.6.3 irlba_2.3.2
[31] DEoptimR_1.0-8 lars_1.2
[33] Rcpp_0.12.18 KernSmooth_2.23-15
[35] DT_0.4 promises_1.0.1
[37] gdata_2.18.0 DDRTree_0.1.5
[39] DelayedArray_0.4.1 limma_3.34.9
[41] vegan_2.5-2 Hmisc_4.1-1
[43] ShortRead_1.36.1 apcluster_1.4.7
[45] RSpectra_0.13-1 msir_1.3.1
[47] mnormt_1.5-5 digest_0.6.15
[49] RMySQL_0.10.15 png_0.1-7
[51] qlcMatrix_0.9.7 cowplot_0.9.3
[53] glmnet_2.0-16 pkgconfig_2.0.1
[55] docopt_0.6 ggbeeswarm_0.6.0
[57] iterators_1.0.10 minqa_1.2.4
[59] lavaan_0.6-2 reticulate_1.10
[61] SummarizedExperiment_1.8.1 spam_2.2-0
[63] beeswarm_0.2.3 modeltools_0.2-22
[65] RcppNumerical_0.3-2 zoo_1.8-3
[67] tidyselect_0.2.4 ZIM_1.0.3
[69] reshape2_1.4.3 purrr_0.2.5
[71] kernlab_0.9-26 ica_1.0-2
[73] pcaPP_1.9-73 EDASeq_2.12.0
[75] viridisLite_0.3.0 snow_0.4-2
[77] rtracklayer_1.38.3 rlang_0.2.1
[79] hexbin_1.27.2 manipulateWidget_0.10.0
[81] glue_1.3.0 metap_1.0
[83] RColorBrewer_1.1-2 registry_0.5
[85] fpc_2.1-11.1 matrixStats_0.54.0
[87] stringr_1.3.1 pkgmaker_0.27
[89] fields_9.6 DESeq2_1.18.1
[91] SparseM_1.77 gbRd_0.4-11
[93] httpuv_1.4.5 class_7.3-14
[95] BPSC_0.99.1 RMTstat_0.3
[97] annotate_1.56.2 webshot_0.5.0
[99] jsonlite_1.5 XVector_0.18.0
[101] bit_1.1-14 mime_0.5
[103] gridExtra_2.3 gplots_3.0.1
[105] Rsamtools_1.30.0 zingeR_0.1.0
[107] stringi_1.2.4 gmodels_2.18.1
[109] gsl_1.9-10.3 bitops_1.0-6
[111] Rdpack_0.9-0 maps_3.3.0
[113] RSQLite_2.1.1 tidyr_0.8.1
[115] pheatmap_1.0.10 data.table_1.11.4
[117] DEDS_1.52.0 energy_1.7-4
[119] rstudioapi_0.7 GenomicAlignments_1.14.2
[121] nlme_3.1-137 qvalue_2.10.0
[123] scran_1.6.9 fastcluster_1.1.25
[125] locfit_1.5-9.1 scone_1.2.0
[127] miniUI_0.1.1.1 cobs_1.3-3
[129] R.oo_1.22.0 prabclus_2.2-6
[131] segmented_0.5-3.0 BiocGenerics_0.24.0
[133] readxl_1.1.0 ROTS_1.6.0
[135] munsell_0.5.0 cellranger_1.1.0
[137] R.methodsS3_1.7.1 moments_0.14
[139] hwriter_1.3.2 caTools_1.17.1.1
[141] codetools_0.2-15 coda_0.19-1
[143] Biobase_2.38.0 GenomeInfoDb_1.14.0
[145] vipor_0.4.5 lmtest_0.9-36
[147] htmlTable_1.12 rARPACK_0.11-0
[149] xtable_1.8-2 SAVER_1.0.0
[151] ROCR_1.0-7 diptest_0.75-7
[153] lpsymphony_1.7.1 abind_1.4-5
[155] FNN_1.1.2 RANN_2.6
[157] sparsesvd_0.1-4 CompQuadForm_1.4.3
[159] GenomicRanges_1.30.3 bibtex_0.4.2
[161] rgl_0.99.16 tibble_1.4.2
[163] ggdendro_0.1-20 cluster_2.0.7-1
[165] Seurat_2.3.4 Matrix_1.2-14
[167] prettyunits_1.0.2 shinyBS_0.61
[169] ggridges_0.5.0 NOISeq_2.22.1
[171] shinydashboard_0.7.0 mclust_5.4.1
[173] igraph_1.2.2 slam_0.1-43
[175] testthat_2.0.0 doSNOW_1.0.16
[177] htmltools_0.3.6 GenomicFeatures_1.30.3
[179] XML_3.98-1.13 DrImpute_1.0
[181] foreign_0.8-71 withr_2.1.2
[183] fitdistrplus_1.0-9 BiocParallel_1.12.0
[185] aroma.light_3.8.0 bit64_0.9-7
[187] rngtools_1.3.1 doRNG_1.7.1
[189] foreach_1.4.4 robustbase_0.93-2
[191] outliers_0.14 scde_2.6.0
[193] Biostrings_2.46.0 combinat_0.0-8
[195] iCOBRA_1.6.0 memoise_1.1.0
[197] VGAM_1.0-5 nonnest2_0.5-1
[199] forcats_0.3.0 rio_0.5.10
[201] geneplotter_1.56.0 permute_0.9-4
[203] curl_3.2 fdrtool_1.2.15
[205] trimcluster_0.1-2.1 acepack_1.4.1
[207] edgeR_3.20.9 checkmate_1.8.5
[209] tensorA_0.36.1 DECENT_0.2.0
[211] ellipse_0.4.1 ggplot2_3.0.0
[213] rjson_0.2.20 openxlsx_4.1.0
[215] ggrepel_0.8.0 distillery_1.0-4
[217] dtw_1.20-1 scDD_1.2.0
[219] stabledist_0.7-1 Lmoments_1.2-3
[221] tools_3.4.3 sandwich_2.4-0
[223] magrittr_1.5 RCurl_1.95-4.11
[225] proxy_0.4-22 car_3.0-0
[227] pbivnorm_0.6.0 ape_5.1
[229] bayesm_3.1-0.1 EBSeq_1.18.0
[231] httr_1.3.1 assertthat_0.2.0
[233] boot_1.3-20 R6_2.2.2
[235] nnet_7.3-12 progress_1.2.0
[237] tximport_1.6.0 genefilter_1.60.0
[239] gtools_3.8.1 statmod_1.4.30
[241] Rook_1.1-1 rhdf5_2.22.0
[243] splines_3.4.3 carData_3.0-1
[245] colorspace_1.3-2 amap_0.8-16
[247] stats4_3.4.3 NBPSeq_0.3.0
[249] compositions_1.40-2 base64enc_0.1-3
[251] baySeq_2.12.0 pillar_1.3.0
[253] HSMMSingleCell_0.112.0 bindrcpp_0.2.2
[255] GenomeInfoDbData_1.0.0 plyr_1.8.4
[257] extRemes_2.0-9 dotCall64_1.0-0
[259] gtable_0.2.0 zip_1.0.0
[261] SCnorm_1.0.0 monocle_2.6.4
[263] knitr_1.20 RcppArmadillo_0.8.600.0.0
[265] latticeExtra_0.6-28 biomaRt_2.34.2
[267] IRanges_2.12.0 ADGofTest_0.3
[269] copula_0.999-18 crosstalk_1.0.0
[271] Cairo_1.5-9 doParallel_1.0.11
[273] pscl_1.5.2 flexmix_2.3-14
[275] quantreg_5.36 AnnotationDbi_1.40.0
[277] broom_0.5.0 scales_0.5.0
[279] arm_1.10-1 backports_1.1.2
[281] IHW_1.6.0 S4Vectors_0.16.0
[283] densityClust_0.3 lme4_1.1-17
[285] brew_1.0-6 hms_0.4.2
[287] DESeq_1.30.0 Rtsne_0.13
[289] dplyr_0.7.6 shiny_1.1.0
[291] grid_3.4.3 numDeriv_2016.8-1
[293] bbmle_1.0.20 lazyeval_0.2.1
[295] dynamicTreeCut_1.63-1 Formula_1.2-3
[297] tsne_0.1-3 blockmodeling_0.3.1
[299] crayon_1.3.4 MAST_1.4.1
[301] RUVSeq_1.12.0 viridis_0.5.1
[303] rpart_4.1-13 zinbwave_1.0.0
[305] compiler_3.4.3
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