Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:07 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the GSCA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSCA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 855/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GSCA 2.29.0 (landing page) Zhicheng Ji
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: GSCA |
Version: 2.29.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GSCA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GSCA_2.29.0.tar.gz |
StartedAt: 2023-02-07 03:51:28 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 03:55:50 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 262.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GSCA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GSCA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GSCA_2.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GSCA.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘GSCA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GSCA’ version ‘2.29.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'shiny', 'sp', 'gplots', 'ggplot2', 'reshape2', 'RColorBrewer', 'rhdf5' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GSCA’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘Affyhgu133A2Expr’ ‘Affyhgu133Plus2Expr’ ‘Affyhgu133aExpr’ ‘Affymoe4302Expr’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GSCA: no visible global function definition for ‘data’ GSCA: no visible binding for global variable ‘Affyhgu133aExprtab’ GSCA: no visible binding for global variable ‘Affymoe4302Exprtab’ GSCA: no visible binding for global variable ‘Affyhgu133A2Exprtab’ GSCA: no visible binding for global variable ‘Affyhgu133Plus2Exprtab’ GSCA: no visible binding for global variable ‘geneid’ GSCA: no visible global function definition for ‘qnorm’ GSCA: no visible global function definition for ‘sd’ GSCA: no visible global function definition for ‘quantile’ GSCA: no visible global function definition for ‘fisher.test’ GSCAeda: no visible global function definition for ‘data’ GSCAeda: no visible binding for global variable ‘Affyhgu133aExprtab’ GSCAeda: no visible binding for global variable ‘Affymoe4302Exprtab’ GSCAeda: no visible binding for global variable ‘Affyhgu133A2Exprtab’ GSCAeda: no visible binding for global variable ‘Affyhgu133Plus2Exprtab’ GSCAeda: no visible binding for global variable ‘geneid’ GSCAeda: no visible global function definition for ‘qnorm’ GSCAeda: no visible global function definition for ‘sd’ GSCAeda: no visible global function definition for ‘quantile’ GSCAeda: no visible global function definition for ‘pdf’ GSCAeda: no visible global function definition for ‘str’ GSCAeda: no visible binding for global variable ‘variable’ GSCAeda: no visible binding for global variable ‘value’ GSCAeda: no visible binding for global variable ‘SampleType’ GSCAeda: no visible global function definition for ‘par’ GSCAeda: no visible global function definition for ‘colorRampPalette’ GSCAeda: no visible global function definition for ‘t.test’ GSCAeda: no visible binding for global variable ‘Var1’ GSCAeda: no visible binding for global variable ‘Var2’ GSCAeda: no visible binding for global variable ‘t.stat’ GSCAeda: no visible binding for global variable ‘P.value’ GSCAeda: no visible global function definition for ‘fisher.test’ GSCAeda: no visible global function definition for ‘dev.off’ GSCAeda: no visible global function definition for ‘write.csv’ GSCAeda: no visible global function definition for ‘write.table’ GSCAplot: no visible global function definition for ‘data’ GSCAplot: no visible binding for global variable ‘Affyhgu133aExprtab’ GSCAplot: no visible binding for global variable ‘Affymoe4302Exprtab’ GSCAplot: no visible binding for global variable ‘Affyhgu133A2Exprtab’ GSCAplot: no visible binding for global variable ‘Affyhgu133Plus2Exprtab’ GSCAplot: no visible global function definition for ‘pdf’ GSCAplot: no visible global function definition for ‘par’ GSCAplot: no visible global function definition for ‘hist’ GSCAplot: no visible global function definition for ‘title’ GSCAplot: no visible global function definition for ‘dev.off’ annotatePeaks: no visible binding for global variable ‘allreffile’ tabSearch: no visible global function definition for ‘data’ tabSearch: no visible binding for global variable ‘Affyhgu133aExprtab’ tabSearch: no visible binding for global variable ‘Affymoe4302Exprtab’ tabSearch: no visible binding for global variable ‘Affyhgu133A2Exprtab’ tabSearch: no visible binding for global variable ‘Affyhgu133Plus2Exprtab’ Undefined global functions or variables: Affyhgu133A2Exprtab Affyhgu133Plus2Exprtab Affyhgu133aExprtab Affymoe4302Exprtab P.value SampleType Var1 Var2 allreffile colorRampPalette data dev.off fisher.test geneid hist par pdf qnorm quantile sd str t.stat t.test title value variable write.csv write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "pdf") importFrom("graphics", "hist", "par", "title") importFrom("stats", "fisher.test", "qnorm", "quantile", "sd", "t.test") importFrom("utils", "data", "str", "write.csv", "write.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘GSCA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: tabSearch > ### Title: Searches through GPL96, GPL1261, GPL570 or GPL571 compendium > ### data for biological contexts of interest. > ### Aliases: tabSearch > ### Keywords: search > > ### ** Examples > > library(GSCA) > ## Search for all contexts in GSE7123 in hgu133a > tabSearch("GSE7123","hgu133a") Loading required package: Affyhgu133aExpr ExperimentID SampleType SampleCount 1 GSE7123 pbmc:hepatitis_c,_day_0 59 2 GSE7123 pbmc:hepatitis_c,_day_1 60 3 GSE7123 pbmc:hepatitis_c,_day_2 59 4 GSE7123 pbmc:hepatitis_c,_day_7 60 5 GSE7123 pbmc:hepatitis_c,_day_14 54 6 GSE7123 pbmc:hepatitis_c,_day_28 52 > > ## Search for all contexts labeled 'fetal' or 'liver' in moe4302 > tabSearch(c("Fetal","Liver"),"moe4302") Loading required package: Affymoe4302Expr ExperimentID 1 GSE13044 2 GSE13044 3 GSE13044 4 GSE13044 5 GSE13044 6 GSE13044 7 GSE13044 8 GSE13044 9 GSE13044 10 GSE13044 11 GSE13149 12 GSE13149 13 GSE13149 14 GSE13149 15 GSE13149 16 GSE13149 17 GSE13149 18 GSE13149 19 GSE7342 20 GSE7342 21 GSE7342 22 GSE7342 23 GSE11220;GSE11224 24 GSE11220;GSE11224 25 GSE11220;GSE11224 26 GSE11220;GSE11224 27 GSE11220;GSE11224 28 GSE11220;GSE11224 29 GSE11220;GSE11224 30 GSE11220;GSE11224 31 GSE11220;GSE11224 32 GSE11222;GSE11224 33 GSE11777 34 GSE11777 35 GSE12712;GSE13149;GSE13583;GSE13585;GSE5128;GSE5959;GSE6210;GSE6297;GSE6632;GSE6998;GSE7357;GSE7688;GSE8249;GSE8292;GSE8316;GSE8396;GSE8295;GSE8316;GSE8969;GSE9012;GSE9892;GSE9954;GSE10246;GSE10493;GSE10744;GSE10895;GSE11382;GSE11632;GSE11899 36 GSE12712 37 GSE12712 38 GSE12712 39 GSE12712 40 GSE12712 41 GSE12712 42 GSE12908 43 GSE12908 44 GSE13149 45 GSE13149 46 GSE13149 47 GSE13149 48 GSE13149 49 GSE13333 50 GSE13333 51 GSE13583;GSE13585 52 GSE13583;GSE13585 53 GSE13583;GSE13585 54 GSE13948 55 GSE13948 56 GSE13948 57 GSE13948 58 GSE13948 59 GSE13948 60 GSE13948 61 GSE2060 62 GSE2060 63 GSE2060 64 GSE5128 65 GSE5128 66 GSE5128 67 GSE5128 68 GSE5826 69 GSE6210 70 GSE6210 71 GSE6210 72 GSE6297 73 GSE6297 74 GSE6297 75 GSE6632 76 GSE6632 77 GSE3425 78 GSE3425 79 GSE3889 80 GSE3889 81 GSE6850 82 GSE6850 83 GSE6850 84 GSE6903 85 GSE6903 86 GSE6998 87 GSE6998 88 GSE6998 89 GSE6998 90 GSE6998 91 GSE6998 92 GSE6998 93 GSE6998 94 GSE6998 95 GSE6998 96 GSE6998 97 GSE6998 98 GSE6998 99 GSE6998 100 GSE6998 101 GSE7038 102 GSE7357 103 GSE7357 104 GSE7357 105 GSE7357 106 GSE7357 107 GSE7357 108 GSE8292;GSE8316;GSE8396 109 GSE8292;GSE8316;GSE8396;GSE8295;GSE8316 110 GSE8292;GSE8316;GSE8396 111 GSE8295;GSE8316 112 GSE8295;GSE8316 113 GSE8396 114 GSE8396 115 GSE8396 116 GSE8396 117 GSE8396 118 GSE8396 119 GSE8396 120 GSE8396 121 GSE8396 122 GSE8396 123 GSE8396 124 GSE8396 125 GSE8396 126 GSE8396 127 GSE8396 128 GSE8396 129 GSE7038 130 GSE8753 131 GSE8753 132 GSE8969 133 GSE9012 134 GSE9097 135 GSE9097 136 GSE9338 137 GSE9338 138 GSE9338 139 GSE9338 140 GSE9338 141 GSE9441;GSE9444 142 GSE9441;GSE9444 143 GSE9441;GSE9444 144 GSE9441;GSE9444 145 GSE9441;GSE9444 146 GSE9441;GSE9444 147 GSE9441;GSE9444 148 GSE9441;GSE9444 149 GSE9441;GSE9444 150 GSE9441;GSE9444 151 GSE9441;GSE9444 152 GSE9441;GSE9444 153 GSE9441;GSE9444 154 GSE9441;GSE9444 155 GSE9441;GSE9444 156 GSE9441;GSE9444 157 GSE9441;GSE9444 158 GSE9441;GSE9444 159 GSE9549 160 GSE9549 161 GSE9630 162 GSE9630 163 GSE9630 164 GSE9630 165 GSE9630 166 GSE9630 167 GSE9630 168 GSE9630 169 GSE9630 170 GSE9630 171 GSE9630 172 GSE9630 173 GSE9786 174 GSE9786 175 GSE9786 176 GSE9786 177 GSE9786 178 GSE9786 179 GSE9786 180 GSE9786 181 GSE9786 182 GSE9786 183 GSE9786 184 GSE9786 185 GSE9786 186 GSE9786 187 GSE9786 188 GSE9786 189 GSE9809 190 GSE9809 191 GSE9809 192 GSE9809 193 GSE9809 194 GSE9809 195 GSE9809 196 GSE9809 197 GSE9809 198 GSE9809 199 GSE9892 200 GSE9892 201 GSE9892 202 GSE9892 203 GSE9892 204 GSE9892 205 GSE9892 206 GSE9892 207 GSE10082 208 GSE10082 209 GSE10082 210 GSE10082 211 GSE10377 212 GSE10377 213 GSE10377 214 GSE10377 215 GSE10377 216 GSE10493 217 GSE10493 218 GSE10493 219 GSE10493 220 GSE10493 221 GSE10493 222 GSE10493 223 GSE10493 224 GSE10493 225 GSE10493 226 GSE10493 227 GSE10493 228 GSE10493 229 GSE10493 230 GSE10493 231 GSE10493 232 GSE10493 233 GSE10493 234 GSE10493 235 GSE10493 236 GSE10493 237 GSE10493 238 GSE10493 239 GSE10493 240 GSE10895 241 GSE10904 242 GSE10904 243 GSE10904 244 GSE10904 245 GSE10904 246 GSE11050 247 GSE11050 248 GSE11098 249 GSE11098 250 GSE11201 251 GSE11201 252 GSE11201 253 GSE11201 254 GSE11287 255 GSE11287 256 GSE11382 257 GSE11382 258 GSE11632 259 GSE11899 260 GSE11923 SampleType 1 fetal_lung:normal 2 fetal_liver:normal 3 fetal_lung:5mgkgday_pfoa 4 fetal_liver:5mgkgday_pfoa 5 fetal_lung:10mgkgday_pfoa 6 fetal_liver:10mgkgday_pfoa 7 fetal_liver:1mgkgday_pfoa 8 fetal_lung:1mgkgday_pfoa 9 fetal_lung:3mgkgday_pfoa 10 fetal_liver:3mgkgday_pfoa 11 fetal_liver,_embryonic_day_115:gene_expression_data_from_fetal_liver,_embryonic_day_115 12 fetal_liver,_embryonic_day_125:gene_expression_data_from_fetal_liver,_embryonic_day_125 13 fetal_liver,_embryonic_day_135:gene_expression_data_from_fetal_liver,_embryonic_day_135 14 fetal_liver,_embryonic_day_145:gene_expression_data_from_fetal_liver,_embryonic_day_145 15 fetal_liver,_embryonic_day_155:gene_expression_data_from_fetal_liver,_embryonic_day_155 16 fetal_liver,_embryonic_day_165:gene_expression_data_from_fetal_liver,_embryonic_day_165 17 fetal_liver,_embryonic_day_175:gene_expression_data_from_fetal_liver,_embryonic_day_175 18 fetal_liver,_embryonic_day_185:gene_expression_data_from_fetal_liver,_embryonic_day_185 19 fetal_liver_e135:fetal_liver_with_p38alpha_knock_out 20 fetal_liver_e135:normal 21 fetal_liver_e155:fetal_liver_with_p38alpha_knock_out 22 fetal_liver_e155:normal 23 placenta:gene_expression_data_from_fetal_placenta_at_e85 24 placenta:gene_expression_data_from_fetal_placenta_at_e90 25 placenta:gene_expression_data_from_fetal_placenta_at_e105 26 placenta:gene_expression_data_from_fetal_placenta_at_e120 27 placenta:gene_expression_data_from_fetal_placenta_at_e135 28 placenta:gene_expression_data_from_fetal_placenta_at_e150 29 placenta:gene_expression_data_from_fetal_placenta_at_e170 30 placenta:gene_expression_data_from_fetal_placenta_at_e190 31 placenta:gene_expression_data_from_fetal_placenta_at_p0 32 placental_and_decidual_tissue:gene_expression_data_from_fetal_placenta_and_maternal_decidua_(undissected)_at_e170 33 e145_fetal_liver_ter119_+_cells:normal 34 e145_fetal_liver_ter119_+_cells:stat5_ko 35 liver:normal 36 liver:rsl_male_mouse_liver_rna 37 liver:rsl_female_mouse_liver_rna 38 liver:rsl1_tg_male_mouse_liver_rna 39 liver:rsl1_tg_female_mouse_liver_rna 40 liver:rsl2_tg_male_mouse_liver_rna 41 liver:rsl2_tg_female_mouse_liver_rna 42 bipotential_mouse_embryonic_liver_cells:aso30a 43 bipotential_mouse_embryonic_liver_cells:scrambled 44 liver:gene_expression_data_from_young_liver,_the_day_of_birth 45 liver:gene_expression_data_from_young_liver,_3_days_after_birth 46 liver:gene_expression_data_from_young_liver,_7_days_after_birth 47 liver:gene_expression_data_from_young_liver,_14_days_after_birth 48 liver:gene_expression_data_from_young_liver,_21_days_after_birth 49 liver:srf_loxp+_alfpcre_male_liver;_control_sample 50 liver:srf_loxploxp_alfpcre_male_liver;_mutant_sample 51 liver:ko1liver 52 liver:ko2liver 53 liver:ko3liver 54 p0617_liver:p0617_liver,_antimir122_(spc3372)_treated,_day_23 55 p0617_liver:p0617_liver,_antimir122_(spc3372)_treated,_day_3 56 p0617_liver:p0617_liver,_antimir122_(spc3372)_treated,_day_9 57 p0617_liver:p0617_liver,_control,_day_3 58 p0617_liver:p0617_liver,_control,_day_9 59 p0621_liver:p0621_liver,_antimir122_(spc3372)_treated,_day_23 60 p0621_liver:p0621_liver,_control,_day_23 61 liver:8_week_old_male_c57bl6j_mouse_was_fasted_for_20_hr_to_induce_camp_signaling_in_hepatocytes_liver_rna_was_extracted_using_trizol_reagent_and_purified_using_the_qiagen_rneasy_kit_targets_were_produced_using_standard_affymetrix_procedures_from_about_5ug_of_total_rna__data_was_analyzed_using_dchip_software_(wwwdchiporg);author:_xinmin,,zhang;keywords_=_liver,_fasting,_camp_induced_genes,_forskolin,_creb_target_genes 62 liver:8_week_old_male_c57bl6j_mouse_was_fasted_for_16_hr_then_given_food_for_4_hr_liver_rna_was_extracted_using_trizol_reagent_and_purified_using_the_qiagen_rneasy_kit_targets_were_produced_using_standard_affymetrix_procedures_from_about_5ug_of_total_rna__data_was_analyzed_using_dchip_software_(wwwdchiporg);keywords_=_liver,_fasting,_camp_induced_genes,_forskolin,_creb_target_genes 63 hepatocytes:primary_hepatocytes_were_prepared_from_8_week_old_male_c57bl6j_mice_forskolin,_a_camp_agonist,_was_added_to_the_medium_and_cells_were_collected_at_0hr,_1hr_and_4hr_after_forskolin_treatment_total_rna_was_extracted_using_the_qiagen_rneasy_kit_targets_were_produced_using_standard_affymetrix_procedures_from_about_5ug_of_total_rna_data_was_analyzed_using_dchip_software_(wwwdchiporg);keywords_=_liver,_fasting,_camp_induced_genes,_forskolin,_creb_target_genes 64 liver:liver_tissue,_gavage_treatment,_13_weeks,_5_days_per_week,_2,3benzofuran,_240_mg_per_kg 65 liver:liver_tissue,_feed_treatment,_13_weeks,_7_days_per_week,_n1naphthyl)ethylenediamine_dihydrochloride,_2000_ppm 66 liver:liver_tissue,_feed_treatment,_13_weeks,_7_days_per_week,_pentachloronitrobenzene,_8187_ppm 67 liver:liver_tissue,_feed_treatment,_13_weeks,_7_days_per_week,_1,5naphthalenediamine,_2000_ppm 68 liver:liver,_7_days_02%_fenofibrate_feeding 69 liver:third_experimental_liver_sample_from_pgc1beta_mouse 70 liver:first_experimental_liver_sample_from_pgc1beta_mouse 71 liver:second_experimental_liver_sample_from_pgc1beta_mouse 72 liver:gene_expression_data_from_liver_of_a_laboratory_mouse_fed_a_chimpanzee_diet_for_two_weeks 73 liver:gene_expression_data_from_liver_of_a_laboratory_mouse_fed_a_fastfood_diet_for_two_weeks 74 liver:gene_expression_data_from_liver_of_a_laboratory_mouse_fed_a_humancafe_diet_for_two_weeks 75 liver:mouse_castrated_uninfected 76 liver:mouse_castrated_infected_h_hepaticus 77 liver:mice_were_treated_with_3x_80mgkg_bodyweightday_antagomir122 78 liver:mice_were_treated_with_3x_80mgkg_bodyweightday_mmantagomir122 79 liver:scd1_knock_out_mice,_liver,_total_rna_processed_to_biotinlabeled_crna 80 liver:scd1_wild_type_mice,_liver,_total_rna_processed_to_biotinlabeled_crna 81 liver:total_rna_was_extracted_from_liver_of_one_apoe_mouse_infected_with_a_control_adenovirus_expressing_gfp 82 liver:total_rna_extracted_from_one_apoe_mouse_infected_wtih_a_control_adenovirus_expressing_gfp 83 liver:total_rna_extracted_from_one_apoe_mouse_infected_wtih_an_adenovirus_expressing_dominant_negative_cjun 84 liver:b6,_hfd_2wks 85 liver:light_tg,_hfd_2wks 86 liver:10weekold_normal_female_liver_sample_at_1_hour_after_23_hepatectomy 87 liver:10weekold_normal_female_liver_sample_at_2_hours_after_23_hepatectomy 88 liver:10weekold_normal_female_liver_sample_at_6_hours_after_23_hepatectomy 89 liver:10weekold_normal_female_liver_sample_at_12_hours_after_23_hepatectomy 90 liver:10weekold_normal_female_liver_sample_at_18_hours_after_23_hepatectomy 91 liver:10weekold_normal_female_liver_sample_at_24_hours_after_23_hepatectomy 92 liver:10weekold_normal_female_liver_sample_at_30_hours_after_23_hepatectomy 93 liver:10weekold_normal_female_liver_sample_at_48_hours_after_23_hepatectomy 94 liver:10weekold_normal_female_liver_sample_at_72_hours_after_23_hepatectomy 95 embryo_liver:liver_sample_from_mouse_embryo_liver_at_105_days_post_conception_(dpc) 96 embryo_liver:liver_sample_from_mouse_embryo_liver_at_115_days_post_conception_(dpc) 97 embryo_liver:liver_sample_from_mouse_embryo_liver_at_125_days_post_conception_(dpc) 98 embryo_liver:liver_sample_from_mouse_embryo_liver_at_135_days_post_conception_(dpc) 99 embryo_liver:liver_sample_from_mouse_embryo_liver_at_145_days_post_conception_(dpc) 100 embryo_liver:liver_sample_from_mouse_embryo_liver_at_165_days_post_conception_(dpc) 101 rlsc_cell_line:resident_liver_stem_cells_(rlscs) 102 liver:liverb6kobiological_rep1 103 liver:liverb6kobiological_rep2 104 liver:liverb6kobiological_rep3 105 liver:liverd2kobiological_rep1 106 liver:liverd2kobiological_rep2 107 liver:liverd2kobiological_rep3 108 liver:liver,_wild_type_mice,_treatment_with_wy14643_for_6h 109 liver:liver,_pparanull_mice,_control_conditions 110 liver:liver,_pparanull_mice,_treatment_with_wy14643_for_6h 111 liver:liver,_wild_type_mice,_treatment_with_wy14643_for_5d 112 liver:liver,_pparanull_mice,_treatment_with_wy14643_for_5d 113 liver:liver_wildtype_c18:1_6h 114 liver:liver_pparaknockout_c181_6h 115 liver:liver_wildtype_c20:5_6h 116 liver:liver_pparaknockout_c205_6h 117 liver:liver_wildtype_c22:6_6h 118 liver:liver_pparaknockout_c226_6h 119 liver:liver_wildtype_fenofibrate_6h 120 liver:liver_pparaknockout_fenofibrate_6h 121 liver:liver_wildtype_control2_6h 122 liver:liver_pparaknockout_control2_6h 123 liver:liver_wildtype_c10:0_6h 124 liver:liver_pparaknockout_c10:0_6h 125 liver:liver_wildtype_c18:2_6h 126 liver:liver_pparaknockout_c18:2_6h 127 liver:liver_wildtype_c18:3_6h 128 liver:liver_pparaknockout_c18:3_6h 129 rlsc_cell_line:wt_e143_resident_liver_stem_cells_(rlscs) 130 liver:liver_tissue_from_c57bl6j_mice_fed_on_highfat_diets 131 liver:liver_tissue_from_c57bl6j_mice_fed_on_control_diet 132 liver:liver,_nrf2_deficient 133 liver:gene_expression_data_from_liver_tumors_of_trim24_ko_mice 134 liver:gene_expression_data_from_normal_mouse_liver;_mouse_liver_to_study_h_hepaticus_infection_and_liver_cancer 135 liver:gene_expression_data_from_h_hepaticus_infected_mouse;_mouse_liver_to_study_h_hepaticus_infection_and_liver_cancer 136 liver:mus_musculus_domesticus 137 liver:mus_musculus_musculus 138 liver:mus_musculus_musculus_x_m_m_domesticus 139 liver:mus_musculus_castaneus 140 liver:mus_musculus_musculus_x_m_m_castaneus 141 liver:akrj,_control,_time_of_sacrifice_zt_6,_replicat_1,_liver 142 liver:akrj,_control,_time_of_sacrifice_zt_0,_replicat_2,_liver 143 liver:akrj,_control,_time_of_sacrifice_zt_0,_replicat_3,_liver 144 liver:akrj,_sleep_deprived,_time_of_sacrifice_zt_6,_replicat_1,_liver 145 liver:akrj,_sleep_deprived,_time_of_sacrifice_zt_6,_replicat_2,_liver 146 liver:akrj,_sleep_deprived,_time_of_sacrifice_zt_6,_replicat_3,_liver 147 liver:c57bl6j,_control,_time_of_sacrifice_zt_6,_replicat_1,_liver 148 liver:c57bl6j,_control,_time_of_sacrifice_zt_6,_replicat_2,_liver 149 liver:c57bl6j,_control,_time_of_sacrifice_zt_6,_replicat_3,_liver 150 liver:c57bl6j,_sleep_deprived,_time_of_sacrifice_zt_6,_replicat_1,_liver 151 liver:c57bl6j,_sleep_deprived,_time_of_sacrifice_zt_6,_replicat_2,_liver 152 liver:c57bl6j,_sleep_deprived,_time_of_sacrifice_zt_6,_replicat_3,_liver 153 liver:dba2j,_control,_time_of_sacrifice_zt_6,_replicat_1,_liver 154 liver:dba2j,_control,_time_of_sacrifice_zt_6,_replicat_2,_liver 155 liver:dba2j,_control,_time_of_sacrifice_zt_6,_replicat_3,_liver 156 liver:dba2j,_sleep_deprived,_time_of_sacrifice_zt_6,_replicat_1,_liver 157 liver:dba2j,_sleep_deprived,_time_of_sacrifice_zt_6,_replicat_2,_liver 158 liver:dba2j,_sleep_deprived,_time_of_sacrifice_zt_6,_replicat_3,_liver 159 liver:socs3_cre_minus 160 liver:socs3_cre_plus 161 liver:sodium_arsenite_added_to_food:_none;_injection:_ip_8hr_saline_only;_diet:_ain76a;_sodium_arsenite_added_to_drinking_water:_none 162 liver:sodium_arsenite_added_to_food:_none;_injection:_none;_diet:_ain76a;_sodium_arsenite_added_to_drinking_water:_100_ppb,_5wk 163 liver:sodium_arsenite_added_to_food:_none;_injection:_none;_diet:_lrd5001;_sodium_arsenite_added_to_drinking_water:_100_ppb,_5wk 164 liver:sodium_arsenite_added_to_food:_none;_injection:_none;_diet:_lrd5001;_sodium_arsenite_added_to_drinking_water:_none 165 liver:sodium_arsenite_added_to_food:_10_ppb,_5wk;_injection:_none;_diet:_ain76a;_sodium_arsenite_added_to_drinking_water:_none 166 liver:sodium_arsenite_added_to_food:_none;_injection:_none;_diet:_ain76a;_sodium_arsenite_added_to_drinking_water:_none 167 liver:sodium_arsenite_added_to_food:_none;_injection:_none;_diet:_ain76a;_sodium_arsenite_added_to_drinking_water:_10_ppb,_5wk 168 liver:sodium_arsenite_added_to_food:_none;_injection:_ip_8hr_1_mgkg_sodium_arsenite,_1_mgkg_dexamethasone_in_saline;_diet:_ain76a;_sodium_arsenite_added_to_drinking_water:_none 169 liver:sodium_arsenite_added_to_food:_10_ppb,_5wk;_injection:_none;_diet:_lrd5001;_sodium_arsenite_added_to_drinking_water:_none 170 liver:sodium_arsenite_added_to_food:_none;_injection:_ip_8hr_1_mgkg_dexamethasone_in_saline;_diet:_ain76a;_sodium_arsenite_added_to_drinking_water:_none 171 liver:sodium_arsenite_added_to_food:_none;_injection:_ip_8hr_1_mgkg_sodium_arsenite_in_saline;_diet:_ain76a;_sodium_arsenite_added_to_drinking_water:_none 172 liver:sodium_arsenite_added_to_food:_none;_injection:_none;_diet:_lrd5001;_sodium_arsenite_added_to_drinking_water:_10_ppb,_5wk 173 liver:wtctr10 174 liver:wtctr11 175 liver:wtctr12 176 liver:wtctr14 177 liver:wtpfoa6 178 liver:wtpfoa9 179 liver:wtpfoa13 180 liver:wtpfoa15 181 liver:koctr3 182 liver:koctr5 183 liver:koctr8 184 liver:koctr16 185 liver:kopfoa1 186 liver:kopfoa2 187 liver:kopfoa4 188 liver:kopfoa7 189 liver:gene_expression_data_from_3_wildtype_female_mice_liver_tissues_at_11_weeks_old 190 liver:gene_expression_data_from_3_wildtype_male_mice_liver_tissues_at_11_weeks_old 191 liver:gene_expression_data_from_3_gnmt__male_mice_liver_tissues_at_11_weeks_old 192 liver:gene_expression_data_from_3_gnmt__female_mice_liver_tissues_at_11_weeks_old 193 liver:gene_expression_data_from_liver_dysplasia_nodules_tissues_of_a_female_gnmt__mouse 194 liver:gene_expression_data_from_liver_dysplasia_nodules_adjacent_tissues_of_a_female_gnmt__mouse 195 liver:gene_expression_data_from_hcc_tissues_of_a_male_gnmt__mouse 196 liver:gene_expression_data_from_hcc_adjacent_tissues_of_a_male_gnmt__mouse 197 liver:gene_expression_data_from_hcc_tissues_of_a_female_gnmt__mouse 198 liver:gene_expression_data_from_hcc_adjacent_tissues_of_a_female_gnmt__mouse 199 liver:tgfb_ko1_(balbc) 200 liver:tgfb_ko2_(balbc) 201 liver:tgfb_ko3_(balbc) 202 liver:infko_tgbf+_(balbc) 203 liver:infko_tgbf+_2_(balbc) 204 liver:infko_tgbf+_3_(balbc) 205 liver:ifnko_tgfb1_ko2_(balbc) 206 liver:ifnko_tgfb1_ko3_(balbc) 207 liver:mouse_liver,_ahr_knockout,_cornoil_treated,_19_hours 208 liver:mouse_liver,_ahr_wildtype,_cornoil_treated,_19_hours 209 liver:mouse_liver,_ahr_wildtype,_1000_ugkg_tcdd_treated,_19_hours 210 liver:mouse_liver,_ahr_knockout,_1000_ugkg_tcdd_treated,_19_hours 211 liver:male_c57bl6j_10_week_old_liver 212 liver:male_balbcbyj_10_week_old_liver 213 liver:male_fvbnj_10_week_old_liver 214 liver:male_nzwlacj_10_week_old_liver 215 liver:male_riiisj_10_week_old_liver 216 liver:strain_129,_females,_hf_diet 217 liver:strain_129,_males,_hf_diet 218 liver:strain_a,_females,_hf_diet 219 liver:strain_a,_males,_hf_diet 220 liver:strain_b6,_females,_hf_diet 221 liver:strain_b6,_males,_hf_diet 222 liver:strain_balb,_females,_hf_diet 223 liver:strain_balb,_males,_hf_diet 224 liver:strain_c3h,_females,_hf_diet 225 liver:strain_c3h,_males,_hf_diet 226 liver:strain_cast,_females,_hf_diet 227 liver:strain_cast,_males,_hf_diet 228 liver:strain_dba,_females,_hf_diet 229 liver:strain_dba,_males,_hf_diet 230 liver:strain_i,_females,_hf_diet 231 liver:strain_i,_males,_hf_diet 232 liver:strain_mrl,_females,_hf_diet 233 liver:strain_mrl,_males,_hf_diet 234 liver:strain_nzb,_females,_hf_diet 235 liver:strain_nzb,_males,_hf_diet 236 liver:strain_pera,_females,_hf_diet 237 liver:strain_pera,_males,_hf_diet 238 liver:strain_sm,_females,_hf_diet 239 liver:strain_sm,_males,_hf_diet 240 liver:genotype:_mfp2_ 241 liver:alb67_mutant_mouse 242 liver:alb69_mutant_mouse 243 liver:alb73_mutant_mouse 244 liver:lox62_control_mouse 245 liver:lox95_control_mouse 246 marmota_monax_liver:woodchuck_liver_tissue_with_no_hcc,_but_surrouding_the_hccs,_mouse_array 247 marmota_monax_liver:woodchuck_liver_hcc_tumor_confirmed_with_ultrasound,_mouse_array 248 liver:liver,_fah,_p21_knockout_mouse_on_ntbc 249 liver:liver,_fah,_p21_knockout_mouse_off_ntbc 250 liver:gene_expression_data_from_105_dpc_mouse_embryonic_(minus_liver)_sample 251 liver:gene_expression_data_from_115_dpc_mouse_embryonic_(minus_liver)_sample 252 liver:gene_expression_data_from_125_dpc_mouse_embryonic_(minus_liver)_sample 253 liver:gene_expression_data_from_145_dpc_mouse_embryonic_(minus_liver)_sample 254 liver:liver,_conditional_keap1_knockout,_albcre::keap1(flox) 255 liver:liver,_genetic_control_albcre:keap1(flox+) 256 liver:female_mouse_liver,_40_wk,_afb1_inoculated 257 liver:female_mouse_liver,_40_wk,_afb1_&_h_hepaticus_inoculated 258 liver:liver_sample_from_a_tmprss6deficient_3monthold_male_mouse 259 liver:mutant 260 liver:na SampleCount 1 10 2 10 3 5 4 5 5 5 6 5 7 5 8 4 9 5 10 5 11 2 12 2 13 2 14 2 15 2 16 2 17 2 18 1 19 3 20 3 21 3 22 3 23 5 24 3 25 3 26 3 27 2 28 3 29 3 30 2 31 2 32 2 33 3 34 3 35 165 36 2 37 2 38 2 39 2 40 2 41 2 42 5 43 5 44 2 45 2 46 1 47 1 48 2 49 3 50 3 51 1 52 1 53 1 54 3 55 3 56 3 57 3 58 3 59 3 60 3 61 1 62 1 63 3 64 3 65 3 66 3 67 3 68 2 69 1 70 1 71 1 72 6 73 6 74 6 75 2 76 2 77 1 78 1 79 10 80 10 81 1 82 4 83 5 84 3 85 3 86 2 87 2 88 2 89 2 90 2 91 2 92 2 93 2 94 2 95 2 96 2 97 2 98 2 99 2 100 2 101 1 102 1 103 1 104 1 105 1 106 1 107 1 108 4 109 9 110 5 111 4 112 4 113 5 114 5 115 5 116 4 117 5 118 5 119 5 120 5 121 4 122 4 123 5 124 5 125 4 126 5 127 5 128 5 129 1 130 1 131 1 132 3 133 5 134 1 135 4 136 2 137 2 138 4 139 2 140 4 141 1 142 1 143 1 144 1 145 1 146 1 147 1 148 1 149 1 150 1 151 1 152 1 153 1 154 1 155 1 156 1 157 1 158 1 159 2 160 3 161 5 162 4 163 5 164 5 165 5 166 5 167 5 168 5 169 5 170 5 171 5 172 5 173 1 174 1 175 1 176 1 177 1 178 1 179 1 180 1 181 1 182 1 183 1 184 1 185 1 186 1 187 1 188 1 189 1 190 1 191 1 192 1 193 1 194 1 195 1 196 1 197 1 198 1 199 1 200 1 201 1 202 1 203 1 204 1 205 1 206 1 207 3 208 5 209 6 210 3 211 1 212 1 213 1 214 1 215 1 216 3 217 3 218 3 219 3 220 3 221 3 222 3 223 2 224 3 225 3 226 3 227 3 228 3 229 3 230 3 231 3 232 3 233 3 234 3 235 3 236 3 237 3 238 3 239 3 240 4 241 1 242 1 243 1 244 1 245 1 246 3 247 3 248 1 249 2 250 1 251 1 252 1 253 1 254 3 255 3 256 2 257 2 258 1 259 5 260 48 > > ## Search for all contexts labeled 'fetal liver' AND in GSE13044 in moe4302 > tabSearch(c("Fetal","GSE13044"),"moe4302","AND") Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GSCA.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/GSCA.Rcheck/00check.log’ for details.
GSCA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GSCA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘GSCA’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GSCA)
GSCA.Rcheck/GSCA-Ex.timings
name | user | system | elapsed | |
ConstructTG | 6.613 | 0.072 | 6.955 | |
GSCA | 86.112 | 2.782 | 98.284 | |
GSCAeda | 5.648 | 0.272 | 7.853 | |
GSCAplot | 30.547 | 1.210 | 33.966 | |
GSCAui | 0.001 | 0.000 | 0.000 | |
Oct4ESC_TG | 0.004 | 0.000 | 0.011 | |
STAT1_TG | 0.001 | 0.000 | 0.002 | |
annotatePeaks | 5.345 | 0.163 | 5.939 | |
geneIDdata | 0.047 | 0.000 | 0.086 | |