| 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 |
##############################################################################
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###
### 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 | |